• Gene Finding
• Sequence comparison
• Protein analysis
• GenomeSequence Explorer
• Search for motifs
• Sequences manipulation

Int. J. Mol. Sci.
2016, 17(8), 1211; doi:10.3390/ijms17081211

Glutathione Transferases Superfamily: Cold-Inducible Expression of Distinct GST Genes in Brassica oleracea

Vijayakumar, H. et al.,
1 Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon 57922, Korea 2 Plant Systems Engineering Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Daejeon 34141, Korea

... Subcellular localization prediction of predicted BoGST proteins was performed using Protcomp 9.0 from Softberry [96]. ...

Journal of Plant Biochemistry and Biotechnology
2016, 25(2), 155-167. DOI: 10.1007/s13562-015-0321-y

Molecular cloning, characterization and three-dimensional structure prediction of Lipoxygenase from Finger millet [Eleusine coracana (L.) Gaertn.] germinating seedlings

Kotapati, K. V. et al.,
Centre for Bioinformatics, School of Life SciencesPondicherry University; Department of BiochemistryYogi Vemana University

... The sub cellular localization of EcLOX was predicted by utilizing different publicly available programs, Plant-mPLoc, EpiLoc, YLoc, ProtComp (http://linux1.softberry.com), TargetP (http://www.cbs.dtu.dk/services/TargetP/), ChloroP ...

Fungal Genetics and Biology
2016, 90, 12-22 http://dx.doi.org/10.1016/j.fgb.2016.03.002

Chasing stress signals–Exposure to extracellular stimuli differentially affects the redox state of cell compartments in the wild type and signaling mutants of Botrytis cinerea

Marschall, R., Schumacher, J., Siegmund, U., Tudzynski, P.
Institut fur Biologie und Biotechnologie der Pflanzen, Westfalische Wilhelms-Universitat, Schlossplatz 8, D-48143 Munster, Germany

... Subcellular localization patterns of proteins were predicted by ProtComp v.9.0 (http://linux1.softberry.com/berry.phtml?topic=protcompan&group=help&subgroup=proloc ...

Journal of Experimental Botany
2016, erw297. doi: 10.1093/jxb/erw297

Rice putative methyltransferase gene OsTSD2 is required for root development involving pectin modification

Qu, L. et al.,
1 National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China 2 College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China

... OsTSD2 is predicted to be localized in the Golgi body (http://www.softberry.com/berry.phtml?topic= protcompan&group=programs&subgroup=proloc; Integral Prediction of protein location: Membrane-bound Golgi with score 7.4), which is consistent with its putative role at the site ...

Fish & shellfish immunology
2016, 50, 297-309. http://dx.doi.org/10.1016/j.fsi.2016.02.009

Abundant members of Scavenger receptors family and their identification, characterization and expression against Vibrio alginolyticus infection in juvenile Larimichthys crocea

He, J., Liu, H., Yang, J., Dong, X., & Wu, C
National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, PR China

... The sub-cellular localization was predicated by tool ProtComp 9.0 (http://www.softberry.com/). ...

PLoS Genet
2016, 12(7), e1006152. http://dx.doi.org/10.1371/journal.pgen.1006152

A High Temperature-Dependent Mitochondrial Lipase EXTRA GLUME1 Promotes Floral Phenotypic Robustness against Temperature Fluctuation in Rice (i>Oryza sativa L.)

Zhang, B. et al.,
State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, the People’s Republic of China, University of Chinese Academy of Sciences, Beijing, the People’s Republic of China

... Among them, TargetP [88] (http://www.cbs.dtu.dk/services/TargetP/) has the best consistency compared with MitoProt II-v1.101 [80] (https://ihg.gsf.de/ihg/mitoprot.html), iPSORT [89] (http://ipsort.hgc.jp/), ProtComp 9.0 (http://linux1.softberry.com/berry.phtmtopic=protcompan&group=help&subgroup=proloc) and WoLF PSORT ...

Journal
2016 http://dx.doi.org/10.1371/journal.pone.0157783

De Novo Transcriptome Analysis of the Common New Zealand Stick Insect Clitarchus hookeri (Phasmatodea) Reveals Genes Involved in Olfaction, Digestion and Sexual Reproduction

Wu C. et al.,
Landcare Research, Auckland, New Zealand, School of Biological Sciences, The University of Auckland, Auckland, New Zealand; New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand

... Signal peptides and sub-cellular locations were identified using SignalP (v4.1) [54] and ProtComp (v9.0) (http://linux1.softberry.com), respectively. ...

Genome biology and evolution
2016, 8(3), 681-704. doi: 10.1093/gbe/evw026

A tale of genome compartmentalization: the evolution of virulence clusters in smut fungi

Dutheil, J. Y. et al.,
1Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany 2German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany

... 2004). Annotation of CSEPs. SignalP version 4.1 was used for signal peptide prediction and ProtComp 9.0 (online version) for localization prediction (http://linux1.softberry.com/berry.phtml). We used two prediction schemes. ...

Journal of Agricultural Science and Technology
2016, 18(4), 1129-1141.

Characterization of a Desiccation Stress Induced Lipase Gene from Brassica napusL

Zhang, H. et al.,
1Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People’s Republic of China. 2Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi; Key Laboratory of Edible Fungi Resources and Utilization (South),Ministry of Agriculture, Shanghai 201403, People’s Republic of China.

... Molecular weight and pI of the deduced protein were detected with DNAStar. Subcellular localization prediction was performed with SoftBerry (http://linux1.softberry.com/berry.phtml) and ChloroP Server (http://www.cbs.dtu.dk/services/ChloroP- 1.1/). ...

Planta
August 2016, Volume 244, Issue 2, pp 505–515 DOI: 10.1007/s00425-016-2520-8

Xyloglucan endo-transglycosylase/hydrolase (XET/H) gene is expressed during the seed germination in Podophyllum hexandrum: a high altitude Himalayan plant

Dogra, V., Sharma, R., Yelam, S.
Biotechnology DivisionCSIR-Institute of Himalayan Bioresource Technology Laboratory of Photosynthesis and Stress SignalingShanghai Center for Plant Stress Biology, CAS

...Subcellular localization was predicted using ProCompv9.0 (http://?linux1.?softberry.?com/?berry.?phtml). Secondary structure ...

Algal Research
2016, 17, 236-243. doi:10.1016/j.algal.2016.05.015

Transcriptome analysis of Chlorella zofingiensis to identify genes and their expressions involved in astaxanthin and triacylglycerol biosynthesis

Huang, W., Ye, J., Zhang, J., Lin, Y., He, M., Huang, J.
a Kunming Institute of Botany, Chinese Academic of Sciences, Kunming, Yunnan Province, PR China b University of Chinese Academic of Sciences, Beijing, PR China

... Protein location prediction by ProtComp (http://linux1.softberry. com) suggested that one of these isoforms, namely T1_Unigene_BMK.22394, may ...

BMC biotechnology
2016, 16(Suppl 1):35 DOI: 10.1186/s12896-016-0261-1

Over-expression of a NAC 67 transcription factor from finger millet (Eleusine coracana L.) confers tolerance against salinity and drought stress in rice

Rahman, H., Ramanathan, V., Nallathambi, J., Duraialagaraja, S., Muthurajan, R.
Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University

... structure (PSIPHRED; http://bioinf.cs.ucl.ac.uk/psipred/); pI/Mw (Compute pI/Mw; http://web.expasy.org/compute_pi/); functional region (PROSITE; http://www.expasy.org/) and subcellular localization (ProtCompv9.0; http://www.softberry.com/ ...

Front Plant Sci.
2016; 7: 215. doi: 10.3389/fpls.2016.00215

Identification and Characterization of the Glucose-6-Phosphate Dehydrogenase Gene Family in the Para Rubber Tree, Hevea brasiliensis

Xiangyu Long, Bin He, Yongjun Fang, and Chaorong Tang
Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences Danzhou, China.

... Online software, ProtComp 9.02, was used to evaluate the presence of a transit peptide, which suggested the localization of HbG6PDH3 in the cytosol, and HbG6PDH1, 2 and 4 in the chloroplast (Table ?Table22)....

Applied microbiology and biotechnology
2016, Volume 100, Issue 16 , pp 7125-7136 DOI: 10.1007/s00253-016-7579-4

SILAC and LC-MS/MS identification of Streptococcus equi ssp. zooepidemicus proteins that contribute to mouse brain microvascular endothelial cell infection

Zhe, M. et al.,
1. College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China 2. Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China

... Softberry ProtComp Neural Nets identification showed that 22 of these 25 proteins were cytoplasmic and the other three were membrane proteins (Table 1). Structural analysis of these three membrane proteins is shown in Fig. ... 2013b; Sun et al. 2016). ...

Gene
2016, 588(2), 173-179. doi:10.1016/j.gene.2016.05.024

Identification and expression of a novel carbonic anhydrase isozyme in the pufferfish Takifugu vermicularis

Sumi, K. R., Nou, I. S., Kho, K. H.
a Department of Fisheries Science, College of Fisheries and Ocean Sciences, Chonnam National University, 50, Daehak-ro, Yeosu, Jeonnam 59626, Republic of Korea b Department of Horticulture, College of Life Science and Natural Resources, Sunchon National University, 255, Jungang-ro, Suncheon-Si, Jeollanam-do, 67922, Republic of Korea

.. were analyzed using ProtParam (http://expasy.org/tools/protparam.html) and the protein location within the cell determined by using Protcomp (http://linux1.softberry.com/berry ...

Front Plant Sci.
2016; 7: 1011. doi: 10.3389/fpls.2016.01011

Group 3 LEA Protein, ZmLEA3, Is Involved in Protection from Low Temperature Stress

Liu, Y., Liang, J., Sun, L., Yang, X., Li, D.
1State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China 2Faculty of Chemistry and Chemical Engineering, Taishan Medical University, Tai’an, China

... 3 http://linux1.softberry.com/ berry.phtml?topic=protcomppl\&group=Programs\&subgroup=proloc. ...

Frontiers in Plant Science
2016, 7: 936. doi: 10.3389/fpls.2016.00936

A Genome-Wide Analysis Reveals Stress and Hormone Responsive Patterns of TIFY Family Genes in Brassica rapa

Saha, G., Park, J. I., Kayum, M. A., Nou, I. S.
Department of Horticulture, Sunchon National University, Suncheon, South Korea

.. The subcellular location of TIFY proteins in B. rapa was determined using ProtComp 9.0 from Softberry (http://linux1.softberry.com/ berry.phtml) and Blast2GO software (http://www.blast2go.de). ...

Plant biotechnology journal
2016, 14(2), 699-708. DOI: 10.1111/pbi.12418

Interspecies gene transfer provides soybean resistance to a fungal pathogen

Langenbach, C. et al.,
Department of Plant Physiology, RWTH Aachen University, Aachen, Germany, BASF Plant Science Company GmbH, Agricultural Center, Limburgerhof, Germany

... Analysis with the subcellular localization tool for plant proteins 'softberry Protcomp 9.0' (http://linux1.softberry.com), correctly predicting 86% of extracellular proteins (Klee and Ellis, 2005), even assigned eight ...

Plant Molecular Biology Reporter
2016, 34(2), 512-523. DOI: 10.1007/s11105-015-0943-1 A Comprehensive Analysis of Carotenoid Cleavage Dioxygenases Genes in Solanum Lycopersicum

Wei, Y. et al.,
1. State key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China 2. Institute of Economic Crop, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China

... An N-terminal sorting signal of the SlCCD genes was inves- tigated using online tool iPSORT (http://ipsort.hgc.jp/). The subcellular localization of the SlCCD family was performed by Wolf PSORT (http://wolfpsort.org/) and ProtComp (http:// linux1.softberry.com/all.htm). ...

Journal of cancer research and therapeutics
2016, 12(1), 58-61. DOI: 10.4103/0973-1482.146083

Bioinformatic analysis of c-Myc target from laryngeal cancer cell gene of laryngeal cancer

Zhang, W. D. et al.,
1 Department of Otorhinolaryngology, People's Hospital of Zhengzhou, Henan, Henan Province, China 2 Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat Sen University, Guangdong, China

... Table 1: Predictive analysis of secondary structure of MTLC protein Click here to view. Sub-cellular localization of c-Myc target from laryngeal cancer cell protein Sub-cellular localization analysis of ProtComp v. 9.0 (Softberry, Inc. ...

Folia biologica
2016, 64(1), 23-29. DOI: http://dx.doi.org/10.3409/fb64_1.23

Identification and characterization of pathogen-response genes (repat) in Spodoptera frugiperda (Lepidoptera: Noctuidae)

Machado, V., Serrano, J., Galian, J.

... www.cbs.dtu.dk/services/ SignalP/). The potential subcellular localization of proteins was V. MACHADO et al. 24 Page 3. predicted using ProtComp Version 9.0 (http:// www.softberry.com). The frequency of each repat EST in ...

American Journal of Potato Research
2016, 1-12. DOI: 10.1007/s12230-016-9525-5

Genome-Wide Analyses of Subtilisin-Like Serine Proteases on Solanum tuberosum

Norero, N. S., Castellote, M. A., de la Canal, L., Feingold, S. E.
1. Laboratorio de Agrobiotecnologia, Instituto Nacional de Tecnologia Agropecuaria (INTA) EEA - Balcarce, Ruta 226, Km 73,5. C.C. 276, (7620), Balcarce, Argentina 2. Instituto de Investigaciones Biologicas (IIB), Universidad Nacional de Mar del Plata (UNMdP), Dean Funes 3350. C.C. 722, (7600), Mar del Plata, Argentina

... 2007). PredoTar V1.3 (https://urgi.versailles.inra.fr/Tools/ Predotar) and ProtComp V9.0 (http://www.softberry.com/berry. phtml?topic=protcompplandgroup=programsandsubgroup= proloc) were used to predict signal sequences to organelles and other subcellular localizations. ...

Frontiers in plant science
2016, 7: 310. doi: 10.3389/fpls.2016.00310

AtHD2D Gene Plays a Role in Plant Growth, Development, and Response to Abiotic Stresses in Arabidopsis thaliana

Han, Z. et al.,
1College of Life Science, Northwest A & F University, Yangling, China 2Department of E-A Information Engineering, Liaoning Institute of Science and Technology, Benxi, China

... In addition, the tool for transmembrane regions and signal peptide sequence analysis, ProtComp 9.0 tool (http://linux1.softberry.com/berry.phtml?topic=protcomppl& group=programs&subgroup= proloc) fuzzy k-nearest neighbors (k-NN) algorithm (version 41.0), and TMHMM ...

Biotechnology & Biotechnological Equipment
2016, 1-8. DOI: 10.1080/13102818.2016.1184588

Molecular characterization, expression pattern and function analysis of the OsHSP90 family in rice

Zhang, H. et al.,
a Key Laboratory of Southwest Crop Genetic Resources and Improvement, Ministry of Education, Rice Institute of Sichuan Agricultural University, Chengdu, China

... We further examined the subcellular localization of the nine rice OsHSP90 members with Softberry ProtComp (http://linux1.softberry.com/berry.phtmL). ...

Plant Biotechnology Journal
Volume 14, Issue 7 July 2016 Pages 1563–1577 DOI: 10.1111/pbi.12520

Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea

Agarwal, G. et al.,
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India School of Plant Biology, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia

... Supplementary information. Phylogeny of HSP90 proteins. HSP90 proteins from all five legumes were analysed in silico for their location in cellular milieu using ProtComp v9.0 of Softberry (http://www.softberry.com/berry.phtml). In ...

Scientific reports
2016; 6: 26323. doi: 10.1038/srep26323

Evolutionary origin of the NCSI gene subfamily encoding norcoclaurine synthase is associated with the biosynthesis of benzylisoquinoline alkaloids in plants

Vimolmangkang, S. et al.,
1Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, P. R. China 2Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand

... alignment was performed using web-based MUSCLE program (http://www.ebi.ac.uk/Tools/msa/ muscle/) and prediction of signal peptide was carried out using SignalP4.1 (http://www.cbs.dtu. dk/services/), WoLF PSORT 24 , and Protcomp 9.0 (http://linux1.softberry.com/berry ...

Parasitology research
2016, 1-13. DOI: 10.1007/s00436-016-5114-2

Bioinformatics analysis and construction of phylogenetic tree of aquaporins from Echinococcus granulosus

Wang, F., Ye, B.
1. Department of Pathogenic Biology, Chongqing Medical University, Chongqing, 400016, People’s Republic of China 2. Research Center for Molecule Medicine and Tumor, Chongqing Medical University, Chongqing, People’s Republic of China

... The conservative structural domain was predicted by Conserved Domain (http://www.ncbi.nlm. nih.gov/cdd/). The subcellular localization was predicted by ProtCompv. 9.0 (http://linux1. softberry.com/berry.phtml?topic=protcompan&group= programs&subgroup=proloc/). ...

Parasitology Research
2016, 1-8. DOI: 10.1007/s00436-016-5166-3

In silico cloning and B/T cell epitope prediction of triosephosphate isomerase from Echinococcus granulosus

Wang, F., Ye, B.
1. Department of Pathogenic Biology, Chongqing Medical University, Chongqing, 400016, China 2. Research Center for Molecule Medicine and Tumor, Chongqing Medical University, Chongqing, China

... The structural domain was predicted by SMART (http://smart.embl-heidelberg. de/). The subcellular localization was predicted by ProtComp v. 9.0 (http://linux1.softberry.com/berry. phtml? topic=protcompan&group=programs&subgroup=proloc/). ...

The Journal of Horticultural Science and Biotechnology
2016, 91(2), 203-209. doi: 10.1080/14620316.2015.1133608

Cloning and expression analysis of three genes encoding ubiquitins in papaya (Carica papaya L.).

Geng, J. J., Shen, Y. H., Yang, F. Y., Li, K., Chen, X. J.
a College of Horticulture Fujian Agriculture and Forestry University, Up and Down Road, Fuzhou 350002, P. R. China b Institute of Genetics and Breeding in Horticultural Plants, Fujian Agriculture and Forestry University, Up and Down Road, Fuzhou 350002, P. R. China

... program (http://us.expasy.org/tools/peptide-mass.html). Sub-cellular localisation was predicted using Softberry software (http://linux1.softberry.com/berry.phtml). The secondary structures and three-dimensional structures of the ...

International journal of molecular sciences
2016, 17(4), 441. doi:10.3390/ijms17040441

Molecular Characterization of MaCCS, a Novel Copper Chaperone Gene Involved in Abiotic and Hormonal Stress Responses in Musa acuminata cv. Tianbaojiao

Feng, X. et al.,
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China

... Signal peptide analysis using ChloroP1.1 software showed that the deduced MaCCS protein contains a chloroplast-targeting peptide like other plant CCSs (Figure 1), which agrees with the prediction results of subcellular localization obtained using the SoftBerry website. ...

Molecular biology reports
2016, 1-12. DOI: 10.1007/s11033-016-4008-9

Molecular cloning and characterization of the MsHSP17.7 gene from Medicago sativa L.

Li, Z. Y. et al.,
Institute of Animal SciencesChinese Academy of Agricultural Sciences

... motif prediction (TMHMM, http://?www.?cbs.?dtu.?dk/?services/?TMHMM-2.?0/?), protein secondary structure analysis (Garnier [v6.0.1]; William Pearson, European Bioinformatics Institute, UK), subcellular location prediction (ProtComp, http://?www.?softberry.?com) and ...

Genome
2016, 59(6), 379-391. doi: 10.1139/gen-2016-0018

Expression of salicylic acid-related genes in Brassica oleracea var. capitata during Plasmodiophora brassicae infection

Manoharan, R. K., Shanmugam, A., Hwang, I., Park, J. I., Nou, I. S.
Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonam 57922, Republic of Korea.

... Further, N-glycosylation sites were predicted using the NetNGlyc 1.0 server (Gupta and Jung 2004). Subcellular localization prediction of predicted MES proteins was performed using Protcomp 9.0 from Softberry (http://linux1.softberry.com/berry.phtml). ...

PlantOmics Journal
2016 DOI:10.21475/poj.160902.p7778x

Isolation, cloning and bioinformatics analysis of ?-amyrin 11-oxidase coding sequence from licorice

Shirazi, Z., Aalami, A., Tohidfar, M., & Sohani, M. M.
1 Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran 2 Department of Biotechnology, Shahid Beheshti University, Tehran, Iran

... Subcellular studies using Softberry and Psort software showed that the activity of this protein is in endoplasmic reticulum. ... The Softberry and TargetP softwares showed the protein has a signal peptide and is located in the secretory pathway (Fig. ...

Biologia Plantarum
2016, 1-9. DOI 10.1007/s10535-016-0618-2

CsWRKY2, a novel WRKY gene from Camellia sinensis, is involved in cold and drought stress responses

Wang, Y. et al.,
1. Tea Science Research Institute, Nanjing Agricultural University, Nanjing, 210095, P.R. China

... CsWRKY2 and other WRKY proteins were subjected to phylogenetic analysis using MEGA 5.05. The online tool WoLF PSORT (http:// wolfpsort.org/) and Softberry ProComp v. 9.0 (http:// linux1.softberry.com/berry) were used to predict CsWRKY2 protein localization. ...

Parasitology research
2015, 114(10), 3759-3766. DOI: 10.1007/s00436-015-4624-7

Characterization of a novel otubain-like protease with deubiquitination activity from Nosema bombycis (Microsporidia)

Wang, Y et al.,
1. State Key Laboratory of Silkworm genome Biology, Southwest University, Chongqing, 400716, China 2. Laboratory of Animal Biology, Chongqing Normal University, Chongqing, 400047, China

... server.?html). The Softberry server (http://?linux1.?softberry.?com/?berry.?phtml?? topic=?protcompan&?group=?programs&?subgroup=?proloc) was used to predict the subcellular localization of NbOTU1. 3D structural ...

Plant biotechnology journal
10 June 2015 DOI: 10.1111/pbi.12418

Interspecies gene transfer provides soybean resistance to a fungal pathogen

Langenbach, C et al.,
Department of Plant Physiology, RWTH Aachen University, Aachen, Germany; BASF Plant Science Company GmbH, Agricultural Center, Limburgerhof, Germany

... Analysis with the subcellular localization tool for plant proteins 'softberry Protcomp 9.0' (http://linux1.softberry.com), correctly predicting 86% of extracellular proteins (Klee and Ellis, 2005), even assigned eight PINGs (PING1/3/4/6/7/8/9/10) to the apoplast and PING2 and PING5 ...

PloS one
Published: May 18, 2015 DOI: 10.1371/journal.pone.0126657

Genome-Wide Analysis of the AP2/ERF Transcription Factors Family and the Expression Patterns of DREB Genes in Moso Bamboo (Phyllostachys edulis)

Wu et al.,
International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People’s Republic of China Hunan Forest Botanical Garden, Changsha, Hunan Province, People’s Republic of China

... pI) and length of the open reading frame (length) for each gene. Subcellular localization was predicted using Softberry (http://linux1.softberry.com/). The AP2/ERF genes in Arabidopsis were searched using the Arabidopsis Information ...

Plant Physiology and Biochemistry
2015, 97, 70-81. doi:10.1016/j.plaphy.2015.09.016

Light response and potential interacting proteins of a grape flavonoid 3?-hydroxylase gene promoter

Sun, R. Z., Pan, Q. H., Duan, C. Q., & Wang, J.
Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China

... Protein structure was predicted using SOPMA (https://npsa-prabi.ibcp.fr/), TargetP 1.1 (http://www.cbs.dtu.dk/services/TargetP), SignalP 4.1 (http://www.cbs.dtu.dk/services/SignalP/), ProtComp 9.0 (http://www.softberry.com/) and WoLF PSORT (http://wolfpsort.org/). 2.3. ...

BMC genomics
2015, 16(1), 1. DOI: 10.1186/s12864-015-2046-7

Genome-wide identification and characterization of the superoxide dismutase gene family in Musa acuminata cv. Tianbaojiao (AAA group)

Feng, X., Lai, Z., Lin, Y., Lai, G., Lian, C.
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University

... Subcellular localizations and putative transit peptides were predicted by SoftBerry (http://?linux1.?softberry.?com/?), ChloroP1.1 (http://?www.?cbs.?dtu.?dk/?services/? ChloroP/?) [33] and MITOPROT (http://?ihg.?gsf.?de/?ihg/?mitoprot.?html) [34]. ...

Plant Physiology and Biochemistry
2015, 92, 92-104. doi:10.1016/j.plaphy.2015.04.013

Molecular characterization of BZR transcription factor family and abiotic stress induced expression profiling in Brassica rapa

Saha, G. et al.,
Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 540-950, South Korea

... Server (GSDS) web tool ( Guo et al., 2007). The subcellular localization of BrBZR proteins was predicted using ProtComp 9.0 from Softberry (http://linux1.softberry. com/berry.phtml). To identify the putative cis-acting regulatory ...

Genetics and molecular research: GMR
2014, 13(1), 117-126. DOI: 10.4238/2014.January.10.2

Molecular cloning, expression, and regulation of the ovalbumin gene in pigeon oviduct epithelial cells

Zhang H. et al.,
1College of Animal Sciences and Technology, Nanjing Agriculture University, Nanjing, Jiangsu, China 2Institute of Animal Husbandry and Veterinary Science

... Pigeon OVA amino acid sequences were predicted based on the open reading frames of the cDNA sequences (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). The transmembrane seg- ments were detected using the Softberry program (http://linux1.softberry.com/berry.phtml). ... ...According to our computational analysis (ProtComp Version 9.0, Softberry), it is an extracellular secretory protein with 3 transmembrane segment residues: 27-47, 233-252, and 292-309....

Developmental & Comparative Immunology
2014, 42(2), 148-158. DOI: 10.1016/j.dci.2013.08.025

Identification and functional analysis of the peptidoglycan recognition protein LD gene in the mosquito, Armigeres subalbatus

Wang S., Beerntsen B. T
Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, United States

... services/SignalP) and transmembrane domain using ProtComp Ver. 8.0 on SoftBerry (http://www.softberry.com). 2.4. Sequence alignments and evolutionary analysis. The predicted AsPGRP-LD protein sequences were aligned ...

Journal of Tropical Crop Science
2014, 1(1). www.j-tropical-crops.com

Cloning and Characterization of P5CS1 and P5CS2 Genes from Saccharum officinarum L. under Drought Stress

Iskandar, H. M., Widyaningrum, D., Suhandono, S.
A Biotechnology Research Institute for Estate Crop, Jalan Taman Kencana No. 1, Bogor, Indonesia Genetics and Molecular Biology Division, School of Life Science and Technology, Institut Teknologi Bandung,

... J Amino acid sequence of protein were s SoP5CS predicted using Bioedit. In order to predict SoP5CS proteins celular localization, we used TargetP and ProtComp from Softberry (www.softberry.com). Realtimeq PCR(RT- PCR)analysis uantitative q ...

BMR BIOLOGY
2014; Volume:1; Article ID: 1; www.bmrjournals.com

In-Silico characterization of New Delhi Metallo-beta-lactamase-1

Vishwakarma S., Sahu S. K., Mishra S. K.
1 Study Center for Biotechnology, Govt. M. S. Golwalkar College, Rewa (M.P.)

... The tool ProtComp Identifying sub- cellular location of protein [22]. (http://linux1.softberry. com/berry.phtml? ... 2010; 38(Database issue):D161-6. 22. http://linux1.softberry.com/berry. phtml ?topic=pcompb&group=programs&sub group=proloc 23. ...

Molecular Breeding
2014, 1-9. DOI:10.1007/s11032-014-0130-3

Molecular cloning and functional analysis of a salt-induced gene encoding an RNA-binding protein in alfalfa

Long R. et al.,
1. Institute of Animal Science, Chinese Academy of Agriculture Science, Beijing, 100193, China 3. College of Prataculture Science, Nanjing Agriculture University, Nanjing, 210095, China

... pl??page=?/?NPSA/?npsa_?hnn.?html). The subcellular localization of MsRBP was analyzed by ProtComp version 9.0 software (http://?linux1.?softberry.?com/? berry.?phtml). Amino acid sequence alignment was carried ...

PloS one
2014, 9(1), e84359 DOI:10.1371/journal.pone.0084359

Novel NAC transcription factor TaNAC67 confers enhanced multi-abiotic stress tolerances in Arabidopsis

Mao, X. et al.,
The Key Laboratory for Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China

... with PREDATOR (http://bioweb.pasteur.fr/seqanal/protein?/intro-uk.html), and the functional region was identified using PROSITE (http://expasy.hcuge.ch/sprot/prosite.htm?l). Subcellular localization was predicted with ProtComp v9.0 software (http://linux1.softberry.com/berry ...

Journal of chemical ecology
2014, 40(1), 63-70. DOI:10.1007/s10886-013-0373-1

A novel fatty acyl desaturase from the pheromone glands of Ctenopseustis obliquana and C. herana with specific Z5-Desaturase activity on myristic acid

Hagstrom, A. K. et al.,
1. Pheromone Group, Department of Biology, Lund University, Solvegatan 37, 223 62, Lund, Sweden 2. The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand

... The C. obliquana and C. herana desaturase sequences were analyzed with the subcellular localization prediction tools Euk- mPLoc 2.0 (Chou and Shen 2010) and ProtComp 9.0 (Softberry, USA). Quantitative RT-PCR and Analysis ...

Archiv Tierzucht
57 (2014) 15, 1-12 DOI:10.7482/0003-9438-57-015

Molecular cloning, sequence characterization, and gene expression profile of a novel water buffalo (Bubalus bubalis) gene: Na⁺, K⁺-ATPase b -subunit (ATP1B2)

Song, S. et al.,
1Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China, 2Domestic Animal Breeding and Crossbreed-improvement Station of Yunnan Province, Kunming, China

... 2004). ProtComp 9.0 (http://www.softberry.com) was employed to predict protein sorting signals and intracellular localization. Secondary structures of deduced AA sequences were predicted by SOPMA (Geourjon & Deleage 1995). TMHMM version 2.0 (Krogh et al. ...

Plant Cell, Tissue and Organ Culture (PCTOC)
Volume 113, Issue 1 , pp 91-101 DOI:10.1007/s11240-012-0254-2

Transcript profiling identifies novel transcripts with unknown functions as primary response components to osmotic stress in wheat (Triticum aestivum L.)

Garg et al.,
1. Department of Bioscience and Biotechnology, Banasthali University, Banasthali, 304022, Rajasthan, India 2. Department of Biotechnology, Faculty of Science, Jamia Hamdard, New Delhi, 110062, India

... al. 2007 ) and ProtComp v. 9.0 from Softberry Inc. (http://linux1.softberry.com/berry. phtml?topic=protcomppl&group=programs&subgroup=proloc) were utilized to predict the sub-cellular localization of the proteins. Prediction ...

Journal of General Plant Pathology
Volume 79, Issue 2 , pp 96-104 DOI:10.1007/s10327-013-0428-8

Analysis of selected singleton transposable elements (SSTEs) and their application for the development of land PATE markers in Magnaporthe oryzae

Zhang et al.,
1. State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China 2. Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China 4. Interdisciplinary Graduate Program in Genetic Engineering, Graduate School, Kasetsart University, Bangkok, 10900, Thailand

... The non-SSTE sequence was analyzed for predicting genes using the prediction program Fgenesh (http://www.softberry.com). ... 2004 ) and Protcomp (http://www.softberry.com). Analysis of P/A polymorphisms of SSTEs at each locus among different isolates. ...

PloS one
October 15, 2013DOI: 10.1371/journal.pone.0077275

The Scutellaria baicalensis R2R3-MYB Transcription Factors Modulates Flavonoid Biosynthesis by Regulating GA Metabolism in Transgenic Tobacco Plants

Yuan Yuan, Chong Wu, Yunjun Liu, Jian Yang, Luqi Huang
National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, China Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China

... is present in the NtPAL gene [25]. The box L sequence in the promoter sequence of NtPAL (GenBank:AB008199) was predicted as ACTTTG using Softberry (linux1.softberry.com). The sequence contains ACTTTG, which has ... ...The localizations of the deduced proteins were predicted on the ProtComp Version 9.0 (http://linux1.softberry.com/berry.phtml??topic=protcompan&group=programs&subgroup=proloc) as well as SubLoc v1.0 ...

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
Volume 1834, Issue 11, November 2013, Pages 2360–2371 DOI:10.1016/j.bbapap.2013.01.030

Sieving through the cancer secretome

Qifeng Lin a, Hwee Tong Tan a, Hannah Soo Rei Lim b, Maxey C.M. Chung a, b
a Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597 Singapore b Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, 117543 Singapore

... Other programs such as Softberry ProtComp 9.0 (http://linux1.softberry.com/berry.phtml?topic= protcompan&group=programs&subgroup=proloc) and KnowPredsite (http://bio-cluster.iis.sinica. edu.tw/kbloc) [29] are reportedly capable of predicting multiple localizations. ...

Plant Cell Reports
Volume 32, Issue 1 , pp 161-171 DOI:10.1007/s00299-012-1350-9

Over-expression of a subgroup 4 R2R3 type MYB transcription factor gene from Leucaena leucocephala reduces lignin content in transgenic tobacco

Sumita Omer, Santosh Kumar, Bashir M. Khan
1. Plant Tissue Culture Division, CSIR-National Chemical Laboratory, Pune, 411008, India 2. Division of Plant Biology, Centenary Campus, Bose Institute, Kolkata, 700054, India

... 2). In silico sub-cellular localization of LlMYB1 protein was predicted to be nuclear using the program ProtComp ver- sion 9.0 (http://www.linux1.softberry.com/berry.phtml? topic= protcomppl&group=programs&subgroup=proloc) accessed from softberry server. ...

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
Volume 1834, Issue 11, November 2013, Pages 2442–2453 DOI:0.1016/j.bbapap.2013.01.039

Bioinformatics tools for secretome analysis

Dario Caccia a, Matteo Dugo b, Maurizio Callari b, c, Italia Bongarzone a,
a Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy b Functional Genomics Core Facility, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy

... org/tools/PRED-TAT. ProtComp, Subcellular localization prediction, +++, FASTA seq (one at a time), HTML, text, http://linux1.softberry.com/berry.phtml?topic=index&group= programs&subgroup=proloc. PSORTb v3.0, Subcellular ...

PloS one
July 23, 2013DOI: 10.1371/journal.pone.007029

Proteomic and Phytohormone Analysis of the Response of Maize (Zea mays L.) Seedlings to Sugarcane Mosaic Virus

Liuji Wu et al.,
Henan Agricultural University and Synergetic Innovation Center of Henan Grain Crops, Zhengzhou, China, Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Zhengzhou, China

... The subcellular locations of the unique proteins identified in this study were determined using Softberry bioinformatics software. Genetic map positions were determined in silico using the Maize GDB http://www.maizegdb.org/. ...

Appl. Environ. Microbiol.
December 2013 vol. 79 no. 24 7646-7653 DOI:10.1128/AEM.02905-13

Glycerol-3-Phosphate Acyltransferase Contributes to Triacylglycerol Biosynthesis, Lipid Droplet Formation, and Host Invasion in Metarhizium robertsii

Qiang Gao, Yanfang Shang, Wei Huang and Chengshu Wang
Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

.. or gaps, and 1,000 bootstrap replicates. Prediction of mrGAT subcellular localization was performed with the program ProtComp (ver. 9.0, Softberry) and TargetP (ver. 1.1) (22). Gene deletion and complementation.For functional ...

Insect Biochemistry and Molecular Biology
Volume 43, Issue 6, June 2013, Pages 510–521 DOI:10.1016/j.ibmb.2013.03.006

Subcellular localization of the fatty acyl reductase involved in pheromone biosynthesis in the tobacco budworm, Heliothis virescens (Noctuidae: Lepidoptera)

Asa K. Hagstrom a, Andrea Walther b, Jurgen Wendland b, Christer Lofstedt a
a Pheromone Group, Department of Biology, Lund University, Solvegatan 37, SE-223 62 Lund, Sweden b Carlsberg Laboratory, Yeast Biology, Gamle Carlsberg Vej 10, DK-1799 Copenhagen V, Denmark

... on known N-terminal signal sequences (Emanuelsson et al., 2000; Emanuelsson et al., 2007), ProtComp that combines several methods of protein localization prediction of sequences containing signal sequences, anchors and other functional peptides (Softberry, USA), PTS1 ...

Environ. Sci. Technol.,
2013, 47 (10), pp 5327–5335 DOI:10.1021/es400113y

Effects of Deficiency and Excess of Zinc on Morphophysiological Traits and Spatiotemporal Regulation of Zinc-Responsive Genes Reveal Incidence of Cross Talk between Micro- and Macronutrients

Ajay Jain †, Bhaskaran Sinilal ‡, Gurusamy Dhandapani †, Richard B. Meagher §, and Shivendra V. Sahi *‡
† National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi-110012, India ‡ Department of Biology, Western Kentucky University, Bowling Green, Kentucky 42101-1080, United States § Department of Genetics, University of Georgia, Fred C. Davison Life Sciences Complex, Athens, Georgia 30602, United States

... Server, were analyzed in databases AtcisDB for identifying transcription factor binding sites(29, 30) and PlantCare for cis-regulatory elements, respectively.(31) Protein level subcellular localization of the ZIPs was predicted by amino acid sequence analysis at softberry.com. ...

Postharvest Biology and Technology
Volume 75, January 2013, Pages 106–113 DOI:10.1016/j.postharvbio.2012.08.005

Catabolism of GABA in apple fruit: Subcellular localization and biochemical characterization of two g-aminobutyrate transaminases

Trobacher et al.,
a Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G 2W1 b Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1

... Several web-based subcellular localization programs were used to assess the potential targeting of the apple GABA-Ts including TargetP (v1.1; http://www.cbs.dtu.dk/services/TargetP/; Emanuelsson et al., 2000), ProtComp (http://linux1.softberry.com/berry.phtml?topic ...

BMC Plant Biology
2013, 13:156 doi:10.1186/1471-2229-13-156

Functional characterisation of three members of the Vitis vinifera L. carotenoid cleavage dioxygenase gene family

Justin G Lashbrooke 1, Philip R Young 1, Samantha J Dockrall 1, Krishnan Vasanth1 2 and Melane A Vivier 1
1 Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa 2 Current address: Department of Botany, Bharathiar University, Coimbatore, TN, 641 046, India

... bioinformatics.psb.ugent.be/plaza/) [27]. The putative sub-cellular localisation of protein sequences were predicted using ProtComp Version 8.0 (http://www.softberry. com/berry.phtml). V. vinifera expressed sequence tags (ESTs ...

mcp
M113.028480. DOI:10.1074/mcp.M113.028480

Linkage of oxidative stress and mitochondrial dysfunctions to spontaneous culture degeneration in Aspergillus nidulans

Li et al.,
Shanghai Institutes for Biological Sciences, CAS, China

... ver. 9.0, http://linux1.softberry.com/ ) and WoLF PSORT (http://wolfpsort.org/) to predict subcellular localizations and InterProScan analysis (www.ebi.ac.uk/Tools/pfa/iprscan/) to classify individual proteins to protein families. Functional ...

Advanced Science, Engineering and Medicine
Volume 5, Number 8, August 2013 , pp. 777-782(6) DOI:10.1166/asem.2013.1358

Cloning of Alcohol Dehydrogenase Gene from Rapeseeds and Correlation with Waterlogging Tolerance Index

Xu et al.,

... Software TargetP 1.1 could not predict a definite subcellular localization of BnADH-1, only pre- dicted other protein. PSORT predicted a weak subcellular localization of BnADH-1 at mitochondrial matrix space. WoLFPSORT20 and Softberry-ProtComp 21 predicted a Adv. Sci. ...

International Journal of Biotechnology and Biochemistry
Volume 9, Number 3 (2013) pp. 293-312 DOI:

Molecular Cloning, Characterization and Expression Analysis of Stress Responsive Dehydrin Genes from Drought Tolerant Horsegram (Macrotyloma uniflorum (Lam.) Verdc.)

Ramya et al.,
Department of Botany, Sri Krishnadevaraya University, Anantapuram, 515 003, India. ?Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 175 Anyang ro, Anyang City, 430-757, Gyeonggi-do, South Korea.

... 71, 79 and 65 respectively. 4.3 Localization of MuDHN1, MuDHN2 and MuDHN3 genes Integral prediction of protein location was analyzed by ProtComp v9.0 (http://linux1.softberry. com/berry). In this study, predicted localization ...

BMC Genomics
2013, 14:343 doi:10.1186/1471-2164-14-343

An integrative “omics” approach identifies new candidate genes to impact aroma volatiles in peach fruit

Sanchez et al.,
1 Instituto de Biologia Molecular y Celular de Plantas (IBMCP), Ingeniero Fausto Elio s/n, Valencia 46022, Spain 2 Instituto Nacional de Tecnologia Agropecuaria (INTA), Ruta N°9 Km 170, San Pedro 2930, Argentine

... Protein sequences were aligned by the clustalW method using the MegAlign software (DNAStar). Transmembrane domains were predicted with TMpred (http://www.ch.embnet.org) and protein localization with ProtComp v9.0 (http://linux1.softberry.com/berry.phtml). ...

Plant Cell Reports
Volume 32, Issue 8 , pp 1289-1298 DOI:10.1007/s00299-013-1443-0

Overexpression of a novel salt stress-induced glycine-rich protein gene from alfalfa causes salt and ABA sensitivity in Arabidopsis

Long et al.,
1. School of Life Science, Chongqing University, Chongqing, China 2. Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China

... Subcellular localization of MsGRP. The online ProtComp version 9.0 program (http://www.softberry. com) was used to predict the subcellular localization. The result predicted by the integral prediction method showed that MsGRP is most likely localized in the extracellular space. ...

Plant Cell, Tissue and Organ Culture (PCTOC)
Volume 115, Issue 3 , pp 443-455 DOI:10.1007/s11240-013-0375-2

Expression of SbSNAC1, a NAC transcription factor from sorghum, confers drought tolerance to transgenic Arabidopsis

Lu et al.,
1. Institute of Crop Science, Chinese Academy of Agricultural Sciences/The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081, China 2. Plant Science and Technology College, Beijing University of Agriculture, Beijing, China

... Subcellular localization of the SbSNAC1 protein. A nucleus-localization signal (NLS) was found in the N-terminal region of the SbSNAC1 protein using the online subcellular localization analysis software (http://linux1.softberry.com/berry.phtml). ...

Plant Molecular Biology
Volume 81, Issue 1-2 , pp 41-56 DOI:10.1007/s11103-012-9981-3

Functions of rice NAC transcriptional factors, ONAC122 and ONAC131, in defense responses against Magnaporthe grisea

Sun et al.,
1. National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, China 2. Samuel Roberts Noble Foundation, Inc., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA

... 2007; Kaneda et al. 2009; Jensen et al. 2008; Wang et al. 2009; Bu et al. 2008; Takasaki et al. 2010). Subcellular localization of ONAC122 and ONAC131 ONAC122 and ONAC131 were predicted to localize in nucleus using ProtComp v9.0 (http://linux1.softberry. com/berry). ...

Malaria Journal
2013, 12:66 http://www.malariajournal.com/content/12/1/66

Expression profile of the Plasmodium falciparum intra-erythrocytic stage protein, PF3D7_1363700

Roberts1 et al.,
1 Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA. 2 Molecular Microbiology and Immunology and Veterinary Pathobiology Joint Graduate Program, University of Missouri, Columbia, MO, USA.

... enter the se- cretory pathway. In support of this prediction, Softberry and PSORTII, two localization programs, predicted PF3D7_1363700 to be either a secreted or plasma mem- brane protein. Based on topology predictions, there ...

The Plant Cell Online
(2013). 25(6), 1946-1959. DOI:10.?1105/?tpc.?113.?113969

The transition from a phytopathogenic smut ancestor to an anamorphic biocontrol agent deciphered by comparative whole-genome analysis

Lefebvre et al.,
aDepartement de Phytologie, Universite Laval, Quebec G1V 0A6, Canada bAgriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland V0H 1Z0, Canada

...TMHMM v2.0 (Krogh et al., 2001) predicted number of transmembrane domains and position according to cleavage site, and finally, correlation to LocDB or PotLocDB ProtComp v9.0 (http://www.softberry.com) databases....

PloS one
(2013). 8(2), e55879. DOI:10.1371/journal.pone.0055879

The NADPH Oxidase Complexes in Botrytis cinerea: Evidence for a Close Association with the ER and the Tetraspanin Pls1

Siegmund, U., Heller, J., van Kann, J. A., & Tudzynski, P.
Institut fuer Biologie und Biotechnologie der Pflanzen, Westfaelische Wilhelms Universitaet Muenster, Muenster, Germany Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands

...as well as Nox1, Nox2 and Nox4 from Homo sapiens were used to predict their cellular localization using ProtComp v. 9.0 (http://linux1.softberry.com/berry.phtml??topic=protcompan&group=programs&subgroup?=proloc)....

Molecular Microbiology
(2013),89: 29–51. DOI:10.1111/mmi.12254

Ustilago maydis natural antisense transcript expression alters mRNA stability and pathogenesis.

Donaldson, M. E. and Saville, B. J.
1Environmental and Life Sciences Graduate Program 2Forensic Science Program, Trent University, Peterborough, ON, Canada

...Furthermore, putative proteins were inspected for N-terminal secretion signals using SignalP v4.0 (Petersen et?al., 2011), TargetP v1.1 (Emanuelsson et?al., 2000), and ProtComp v9.0 (Softberry)...

Journal of Plant Physiology
Volume 169, Issue 10, 1 July 2012, Pages 992–998 DOI: 10.1016/j.jplph.2012.02.018

The AP2-like gene NsAP2 from water lily is involved in floral organogenesis and plant height

Luo et al.,
College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China

... The bar = 200 ?m. View thumbnail images. Subcellular localization of NsAP2 protein. The NsAP2 protein was predicted to be localized at the nucleus through sequence prediction analysis (http://linux1.softberry.com/berry.phtml?topic=proteinloc&prg=ProtComP). ...

Plant Molecular Biology Reporter
December 2012, Volume 30, Issue 6, pp 1283-1290DOI

Molecular Cloning and Characterization of Two 9-Lipoxygenase Genes from Taxus chinensis

Li et al.,
1. Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People’s Republic of China 2. Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China

... Three different programs, Plant- mPLoc (http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/), SignalP (http://www.cbs.dtu.dk/services/SignalP/), and ProtComp (www.softberry.com/berry.phtml), were used for sub- cellular localization prediction based on the identification of ...

Malaria Journal
2012, 11:80 DOI: 10.1186/1475-2875-11-80

Transcript and protein expression profile of PF11_0394, a Plasmodium falciparum protein expressed in salivary gland sporozoites

Schlarman et al.,
1 Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA 2 Molecular Microbiology and Immunology and Veterinary Pathobiology Joint Graduate Program, University of Missouri, Columbia, MO, USA

... Next, additional sequence analysis programs available on the ExPASy Bioinformatics Resource Portal and SoftBerry, such as PSORT and ProtComp, were used to verify that the proteins encoded by the genes were predicted to either be located on the surface and/or secreted ...

Plant growth regulation
2012, vol. 67, no2, pp. 171-184

CsPDR8 and CsPDR12, two of the 16 pleiotropic drug resistance genes in cucumber, are transcriptionally regulated by phytohormones and auxin herbicide in roots

Migocka M. (1) ; Papierniak A. (1) ; Warzybok A. (1) ; Klobus G. (1)
(1) Department of Plant Physiology, Institute of Plant Biology, Wroclaw University, 50-328, Wroclaw, Poland

... 0 software (Tamura et al. 2011) with bootstraps 1,000. The prediction of subcellular localization was performed using ProtComp v8.0 (softberry.com), whereas TMHMM method (Sonnhammer et al. 1998), based on a hidden ...

Plant Cell Reports
September 2012, Volume 31, Issue 9, pp 1737-1746 DOI: 10.1007/s00299-012-1287-z

An alfalfa (Medicago sativa L.) ethylene response factor gene, MsERF11, enhances salt tolerance in transgenic Arabidopsis

Tingting Chen et al.,
1. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People’s Republic of China 2. Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya’an, 625014, People’s Republic of China

... Subcellular localization of the MsERF11 protein Subcellular localization of the MsERF11 protein was first carried out in silico using an online prediction program ProtComp Version 9.0 (http://linux1.softberry.com/berry.phtml). ...

Advanced Science Letters
Volume 10, Number 1, May 2012 , pp. 191-195(5) DOI: 10.1166/asl.2012.3742

A New Member of PAL Family Initiating Secondary Metabolism During Fatty Acid Biosynthesis in Camellia Oleifera Seeds

X Tan, H Chen, D Zhang, F Hu

... 281, and three transmembrane regions distributed at N-terminal of the protein. The sub-cellular location result predicted by Softberry revealed Co-PAL deposit in cytoplasmid. As shown as in Figure 3, it could be found that -helix ...

Journal of Integrative Agriculture
Volume 11, Issue 1, January 2012, Pages 31–42 DOI: 10.1016/S1671-2927(12)60780-9,

Molecular Characterization and Expression Analysis of TaZFP15, a C₂H₂-Type Zinc Finger Transcription Factor Gene in Wheat (Triticum aestivum L.)

Zhao-hua SUN a, Chang-huan DING a, Xiao-juan LI a, , , Kai XIAO b,
a College of Life Science, Agricultural University of Hebei, Baoding 071001, P.R. China b College of Agronomy, Agricultural University of Hebei, Baoding 071001, P.R. China

... 2). Based on analysis by SubLoc v1.0 www Server.url program and online analy- sis (http://linux1.softberry.com/berry.phtml), the sub- cellular location of TaZFP15 was predicted to be tar- geted onto the nucleus. ... 1.0 program (http://linux1. softberry.com/berry.phtml). ...

Molecular Biology Reports
September 2012, Volume 39, Issue 9, pp 9167-9177 DOI: 10.1007/s11033-012-1789-3

Analysis on DNA sequence of goat RFRP gene and its possible association with average daily sunshine duration

D. W. Huang et al.,
1. Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People’s Republic of China 2. State Key Laboratory of Agricultural Biotechnology, China Agricultural University, Beijing, 100193, People’s Republic of China

... Protein struc- ture and function prediction were performed using Pep- stats (http://www.ebi.ac. uk/Tools/emboss/pepinfo/), PSO RT II Prediction (http://psort.hgc.jp/form2.html), ProtComp 9.0 (http://linux1.softberry.com/berry.phtml?topic= protcompan&group=programs&subgroup ...

Molecular Biology Reports
DOI: 10.1007/s11033-012-1577-0

Isolation and characterization of two hydroperoxide lyase genes from grape berries

Bao-Qing Zhu et al.,
1. Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China

... Sal I (for reverse primer) Mol Biol Rep 123 Page 4. PSORT (http://psort.ims.u-tokyo. ac.jp/), ChloroP 1.1 (http: //www.cbs.dtu.dk) and ProtComp (http://linux1.softberry. com/berry.phtml). The multiple sequence alignments of plant ...

PLoS ONE
7(4): e33731. doi:10.1371/journal.pone.0033731

The Predicted Secretome of the Plant Pathogenic Fungus Fusarium graminearum: A Refined Comparative Analysis

Brown NA, Antoniw J, Hammond-Kosack KE
Centre for Sustainable Pest and Disease Management, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom

... GPI-anchor proteins were predicted by big-PI (http://mendel.imp.ac.at/gpi/cgi-bin/gpi_?pred_fungi. cgi) [48]. ProtComp was also used to predict localization of the remaining proteins using the LocDB and PotLocDB databases (ProtComp v8.0; http://www.softberry.com). ...

Fungal diversity
2012, vol. 54, no 1, pp. 87-99 DOI: 10.1007/s13225-012-0169-6

First characterization of endophytic Corynespora cassiicola isolates with variant cassiicolin genes recovered from rubber trees in Brazil

Deon et al.,
(1) CIRAD, UMR AGAP, 63000, Clermont-Ferrand, France (2) Clermont Universite, Universite Blaise Pascal, UMR 547 PIAF, 63000, Clermont-Ferrand, France

... protein (Krogh et al. 2001). The ProtComp program (version 9.0; http://www.softberry. com) was used to predict the subcellular localization of the protein. Gene expression analyses by real-time PCR RNA extraction and cDNA ...

Plant Cell Reports
Volume 31, Issue 8 , pp 1473-1484 DOI: 10.1007/s00299-012-1262-8

ZmHSP16.9, a cytosolic class I small heat shock protein in maize (Zea mays), confers heat tolerance in transgenic tobacco

Liping Sun et al.,
1. State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, 61 Daizong Street, Tai’an, 271018, Shandong, China 2. Taishan Medical University, Tai’an, 271000, Shandong, China

... 2). In order to further confirm that ZmHSP16.9 belongs to cytosolic sHSP family, the amino acid sequence of ZmHSP16.9 was analyzed in the ProtComp v.9.0 database (http://linux1.softberry. com/berry.phtml?topic=protcomppl &group=programs&subgroup=proloc). ...

Molecular Biology Reports
Volume 39, Issue 3 , pp 2337-2345 DOI: 10.1007/s11033-011-0984-y

Molecular cloning and characterization of an F-box family gene CarF-box1 from chickpea (Cicer arietinum L.)

Yuying Jia et al.,
1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China 2. Key Laboratory of Agricultural Biotechnology, Xinjiang Agricultural University, Urumqi, 830052, China

... proteins [42, 43]. But only one study reported that KFB protein LKP2 located in nuclei [33]. In this study, CarF-box1 was predicted to be located in the nucleus by ProtComp 6.1 (http://linux1.softberry.com/berry). To con- firm this ...

Biologia Plantarum
Volume 56, Issue 1 , pp 43-49 DOI: 10.1007/s10535-012-0014-5

Molecular cloning and characterization of a novel stress responsive gene in alfalfa

Long et al.,
1. College of Animal Science and Technology, China Agriculture University, Beijing, 100191, P.R. China 2. Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, P.R. China

... 5). The position of the nucleus was visualized under laser scanning confocal microscope. In addition, we also used ProtComp v. 9.0 program online (www.softberry.com) to predict the subcellular localization, and the result showed that MsPBL most probably localized in nucleus. ...

BioMetals
Volume 25, Issue 2 , pp 275-283 DOI: 10.1007/s10534-011-9501-y

Identification and characterization of a novel outer membrane protein receptor required for hemin utilization in Vibrio vulnificus

Shreya Datta, Jorge H. Crosa
1. Department of Molecular Microbiology and Immunology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA

... 2010) and ProtCompB (http:// linux1.softberry.com/berry.phtml?topic=protcompan &group=programs&subgroup) computational tools that are commonly used to predict subcellular local- ization of proteins in Gram-negative bacteria. ...

Gene
Volume 502, Issue 1, 1 July 2012, Pages 69–74 DOI: 10.1016/j.gene.2012.04.017

CsNAM-like protein encodes a nuclear localized protein and responds to varied cues in tea [Camellia sinensis (L.) O. Kuntze]

Asosii Paul a, 1, Richard Chalo Muoki a, b, 1, 2, Kashmir Singh b, Sanjay Kumar a
a Biotechnology Division, Council of Scientific and Industrial Research-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh-176061, India b Biotechnology Department, Panjab University, Chandigarh-160014, Punjab, India

... and [Peng et al., 2009]). In this study, CsNAM-like protein was expected to be localised in the nucleus as predicted by the analyses using PSORTII and ProComp v8.0 (http://linux1.softberry.com/berry). To confirm the localization ...

AJCS
6(4):649-655 (2012)

Molecular cloning and expression of 12-oxophytodienoic acid reductase gene from barley

Saeid Abu-Romman
Department of Biotechnology, Faculty of Agricultural Technology, Al-Balqa’ Applied University, Al-Salt, 19117, Jordan

... The amino acids sequence of HvOPR1 was deduced and analyzed with ProtParam tool (http://cn.expasy.org/tools/ protparam.html), and the prediction of subcellular localization was performed using the online tool ProtComp 9.0 (http://linux1.softberry.com/berry.phtml). ...

Journal of Plant Physiology
Volume 169, Issue 18, 15 December 2012, Pages 1807–1814 DOI: 10.1016/j.jplph.2012.07.014,

Characterization of a type-A response regulator differentially expressed during adventitious caulogenesis in Pinus pinaster

Jose M. Alvarez a, Millan Cortizo a, 1, Ricardo J. Ordas a, b
a Laboratorio de Biotecnologia Agroforestal, Escuela Politecnica de Mieres, Universidad de Oviedo, C/Gonzalo Gutierrez Quiros, 33600 Mieres, Spain b Area de Fisiologia Vegetal, Departamento BOS, Universidad de Oviedo, C/Catedratico Rodrigo Uria s/n, 33071 Oviedo, Spain

... The PipsRR1 protein was predicted to be nuclear (ProtComp 9.0 software, http://www.softberry. com). The receiver domain of PipsRR1, PipiRR1 and all of the Arabidopsis type-A RRs (RR 3–9 and RR 15–17) were aligned with the ClustalW software (Fig. ...

BMC Genomics x
BMC Genomics 2012, 13:221 doi:10.1186/1471-2164-13-221

Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses

Dibari et al.,
1 INRA - UMR 1095 ‘Genetique Diversite Ecophysiologie des Cereales’ (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France 2 INRA - Centre National de Ressources Genomiques Vegetales (CNRGV), Chemin de Borde Rouge BP 52627, 31326, Castanet Tolosan cedex, France

...However, according to ProtComp 9.0 [35] prediction, wheat PSY3 may have a putative chloroplast localization....

Plant Molecular Biology
Volume 81, Issue 1-2 , pp 41-56 DOI: 10.1007/s11103-012-9981-3

Functions of rice NAC transcriptional factors, ONAC122 and ONAC131, in defense responses against Magnaporthe grisea

Sun et al.,
1. National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, China 2. Samuel Roberts Noble Foundation, Inc., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA

... 2007; Kaneda et al. 2009; Jensen et al. 2008; Wang et al. 2009; Bu et al. 2008; Takasaki et al. 2010). Subcellular localization of ONAC122 and ONAC131 ONAC122 and ONAC131 were predicted to localize in nucleus using ProtComp v9.0 (http://linux1.softberry. com/berry). ...

BMC Genomics
2012, 13:544 doi:10.1186/1471-2164-13-544

Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis

Katiyar et al.,
1 National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India 2 National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India

...and ProtComp 9.0 server ( http:/ / linux1.softberry.com/ berry.phtml?topic=protcomppl&group= programs&subgroup=proloc webcite). ...

PLoS ONE
7(12): e49904. doi:10.1371/journal.pone.0049904

Defining the Predicted Protein Secretome of the Fungal Wheat Leaf Pathogen Mycosphaerella graminicola

Morais do Amaral A, Antoniw J, Rudd JJ, Hammond-Kosack KE
Embrapa LabEx Programme, Rothamsted Research, Harpenden, Herts, United Kingdom, Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, United Kingdom

...ProtComp was also used to predict localization of the remaining proteins using the LocDB and PotLocDB databases (ProtComp v8.0; http://www.softberry.com)....

Molecular Biology Reports
Volume 39, Issue 2 , pp 1713-1720 DOI 10.1007/s11033-011-0911-2

Identification and expression pattern of one stress-responsive NAC gene from Solanum lycopersicum

Qinqin Han et al.,
1. Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China 2. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

... affrc.go.jp/PLACE/index.html). Subcellular location of protein was predicted with ProComp v8.0 (http://linux1. softberry.com/berry). Multiple sequence alignment was performed using the ClustalW (http://www.ch.embnet.org /software/ClustalW.html). ...

BMC Genomics
2012 13(243). DOI: 10.1186/1471-2164-13-243

The genes and enzymes of the carotenoid biosynthetic pathway in Vitis vinifera L.

Young et al.,
Research and Innovation Centre. Genomics and Biology of Fruit Crops Department

... 1 cTP: Softberry ProtComp (http://www.softberry.com/berry.phtml) prediction for a chloroplast transit peptide 2 The size in base pairs of the cDNA copy of the gene from the predicted ATG to the predicted STOP codon; 3 The size in base pairs of the genomic copy of the gene from ...

POJ
5(2):94-102 (2012)

Genome-wide analysis of cytosolic and chloroplastic isoforms of glutathione reductase in plant cells

Ahmad Tahmasebi 1, Farzaneh Aram 2, Mansour Ebrahimi 3, Manijeh Mohammadi-Dehcheshmeh 4, Esmaeil Ebrahimie 1&5*
1Department of Crop Production & Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran 2Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz University, Shiraz, Iran

...Genomic sequences were also analyzed in the FGENESH gene structure prediction program (http://www.softberry.com) and GeneMark program (http://opal.biology.gatech.edu/GeneMark).... ...Protein sorting and subcellular localization predictions were performed according to ProtComp program Version 5 (http://www.softberry.com/)...

Plant Cell Reports
October 2012 DOI 10.1007/s00299-012-1350-9

Over-expression of a subgroup 4 R2R3 type MYB transcription factor gene from Leucaena leucocephala reduces lignin content in transgenic tobacco

Sumita Omer (1) Santosh Kumar (1) (2) Bashir M. Khan (1)
1. Plant Tissue Culture Division, CSIR-National Chemical Laboratory, Pune, 411008, India 2. Division of Plant Biology, Centenary Campus, Bose Institute, Kolkata, 700054, India

... 2). In silico sub-cellular localization of LlMYB1 protein was predicted to be nuclear using the program ProtComp ver- sion 9.0 (http://www.linux1.softberry.com/berry.phtml? topic= protcomppl&group=programs&subgroup=proloc) accessed from softberry server. ...

Molecular Biology Reports
Volume 39, Issue 4 , pp 3565-3572 DOI 10.1007/s11033-011-1130-6

Identification and characterization of a LEA family gene CarLEA4 from chickpea (Cicer arietinum L.)

Hanyan Gu et al.,
1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China 2. Key Laboratory of Agricultural Biotechnology, Xinjiang Agricultural University, Urumqi, 830052, China

... For protein locali- zation analysis, ProtComp 6.1 (a program for identification of sub-cellular localization of eukaryotic proteins) (http:// linux1.softberry.com/berry.phtml?topic= protcompl&subgroup = programs&subgroup = proloc) and Subloc (Subcellular locali- zation) ...

Journal of Medical Entomology,
2012, Volume 49, Number 3, Pages 441-786 , pp. 656-671(16), DOI: http://dx.doi.org/10.1603/ME11165

Cloning and Characterization of the Peptidoglycan Recognition Protein Genes in the Mosquito, Armigeres subalbatus (Diptera: Culicidae)

Wang, Songjie; Conant, Gavin C.; Ou, Ruguang; Beerntsen, Brenda T.

... The AsPGRP protein sequences were analyzed for the presence of a signal peptide using SignalP 3.0 (http://www.cbs.dtu.dk/services/SignalP) and transmembrane domain using ProtComp Ver. 8.0 on SoftBerry (http://www.softberry.com). ...

Am J Trop Med Hyg
2012 vol. 86 no. 6 943-954 doi: 10.4269/ajtmh.2012.11-0797

PFE_0565w, a Plasmodium falciparum Protein Expressed in Salivary Gland Sporozoites

Schlarman et al.,
Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri; Molecular Microbiology and Immunology and Veterinary Pathobiology Joint Graduate Program, University of Missouri, Columbia, Missouri; Department of Global Health, University of South Florida, Tampa, Florida

... Next, additional sequence analysis programs available on the ExPASy Bioinformatics Resource Portal (www.expasy.org) and SoftBerry (www.softberry.com), such as PSORT and ProtComp, were used to verify that the proteins encoded by the genes were predicted to either be ...

Genet. Mol. Res.
11 (4): 3676-3687 (2012) DOI http://dx.doi.org/10.4238/2012.August.17.3

Regulation of ATG6/Beclin-1 homologs by abiotic stresses and hormones in rice (Oryza sativa L.)

R.M. Rana1,2, S. Dong1, Z. Ali3,4, J. Huang1 and H.S. Zhang1
1State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China 2Department of Plant Breeding and Genetics, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan

... Genomic and cDNA sequences of these proteins were retrieved from NCBI, and gene structure was predicted by FGENESH+ (http://linux1.softberry.com/ berry.phtml). The chromosomal location of each ATG6 gene in rice was determined from the rice physical map constructed by the International Rice Genome Sequencing Project (IRGSP) (http://rgp.dna.affrc.go.jp). Subcellular localization of the OsATG6 family was predicted by WoLF PSORT (Horton et al., 2006) and ProtComp (http://linux1.softberry.com/berry.phtml). ...

Gene
Volume 485, Issue 1, 1 October 2011, Pages 53–62 DOI: 10.1016/j.gene.2011.06.012

Novel genes specifically expressed during the development of the male thalli and antheridia in the dioecious liverwort Pellia endiviifolia

Sierocka et al.,
a Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 89 Umultowska Street, 61-614 Poznan, Poland b Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 89 Umultowska Street, 61-614 Poznan, Poland

... The subcellular location of predicted amino acid sequences was assigned with PSORT (http://psort.imsekundu-tokyo.ac.jp/form.html), TargetP 1.1 (http://www.cbsekunddtu.dk/services/ TargetP/) and ProtComp (http://linux1.softberry.com/berry.phtml?topic=protcompplandgroup ...

Insect Biochemistry and Molecular Biology
Volume 41, Issue 12, December 2011, Pages 956–967 DOI: 10.1016/j.ibmb.2011.09.005,

Functional characterization of ecto-5?-nucleotidases and apyrases in Drosophila melanogaster

Michaela Fenckova a, Radka Hobizalova a, Zdenek Faltynek Fric b, Tomas Dolezal a
a Faculty of Science, University of South Bohemia, Branisovska Street 31, Ceske Budejovice 37005, Czech Republic b Institute of Entomology, Biology Centre of the Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic

... 3; analyzed by SignalP 3.0 and SoftBerry ProtComp v. 9.0). Full-size image (30 K) Full-size image (30 K) Fig. 1. Gene structure of 5 loci with putative Ecto-5?-Nucleotidases. Three chromosomal regions with cytolocations marked in black boxes are shown. ...

Gene
485 (2011) 53–62 DOI: 10.1016/j.gene.2011.06.012

Novel genes speci?cally expressed during the development of the male thalli and antheridia in the dioecious liverwort Pellia endiviifolia

Sierocka et al.,
a Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 89 Umultowska Street, 61-614 Poznan, Poland b Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 89 Umultowska Street, 61-614 Poznan, Poland

... de/) programs. The subcellular location of predicted amino acid sequences was assigned with PSORT (http://psort.imsekundu- tokyo.ac.jp/form.html), TargetP 1.1 (http://www.cbsekunddtu. dk/ services/TargetP/) and ProtComp (http://linux1.softberry.com/berry. ...

POJ
4(5):239-249(2011)

Comparative analysis of the genomic regions flanking Xa21 locus in indica and japonica ssp. of rice (Oryza sativa L.)

Kumar et al.,
1Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli Prof. C.R. Rao Road , Hyderabad 500046, India 2Department of Plant Pathology, Directorate of Rice Research, Rajendranagar, Hyderabad 500030, India

... Protcomp V 8.0 (http://linux1.softberry.com/ berry.phtml) analysis for the sub cellular location of proteins showed that 80% of the predicted TEs were nuclear in localization while the remaining were cytoplasmic or mitochondrial in both the rice lines (Table 9). GC Content in the ... ...Gene prediction from the 100 kb region flanking to Xa21 locus of chromosome 11 in japonica and indica rice was carried out using HMM based gene structure prediction software FGENESH tool (www.softberry.com) trained for monocot plant species (Salamov and Solovyer, 2000) ...

BMC Biotechnology
2011, 11:65 doi:10.1186/1472-6750-11-65

A novel subtilase with NaCl-activated and oxidant-stable activity from Virgibacillus sp. SK37

Ekkarat Phrommao 1, Jirawat Yongsawatdigul 1, Sureelak Rodtong 2 and Montarop Yamabhai 3
1 School of Food Technology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Nakhon Ratchasima, 30000, Thailand 2 School of Microbiology, Institute of Science, Suranaree University of Technology, 111 University Avenue, Nakhon Ratchasima, 30000, Thailand

... AprX-SK37 lacks a canonical signal sequence for membrane translocation (signal peptide) at its N-terminus, indicating an intracellular location as suggested by sub-cellular prediction servers of SignalP 3.0 [24] and ProtCompB (Softberry Bioinformatics tools: http://linux1 ...

Biochemical Genetics
Volume 49, Issue 9-10 , pp 656-664 DOI: 10.1007/s10528-011-9440-x

Cloning and Expression of One Chloroplastic Ascorbate Peroxidase Gene from Nelumbo nucifera

Dong et al.,
1. Key Lab of the Ministry of Education for Plant Developmental Biology, College of Life Science, Wuhan University, Wuhan, 430072, China 2. Lotus Center, Wuhan University, Wuhan, 430072, China

... Subcellular APX was located using the Prot- Comp Version 6.1 program (http://linux1. softberry.com/cgi-bin/programs/proloc/ protcomppl.pl). The amino acid sequence of N. nucifera APX was compared with other species available in GenBank. ...

Biologia
Volume 66, Issue 5 , pp 828-832 DOI: 10.2478/s11756-011-0101-7

Expression analysis of nuclear W2-containing homologs of eukaryotic initiation factors in rice

Peipei Nie, Xiaoyu Li, Yaoguang Liu, Qunyu Zhang
1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Wushan, Guangzhou, 510642, Guangdong, People’s Republic of China

... Subcellular localization of the rice W2 proteins was predicted in silico using the programs WoLF PSORT (Hor- ton et al. 2007) (http://www.genscript.com/psort/wolf psort.html) and ProtComp8.0 (http://linux1.softberry.com/ berry.phtml). ...

Enzyme and Microbial Technology
Volume 49, Issues 6–7, 10 December 2011, Pages 540–546 DOI: 10.1016/j.enzmictec.2011.06.002

Engineered tobacco and microalgae secreting the fungal laccase POXA1b reduce phenol content in olive oil mill wastewater

Zhang et al.,
a Department of Soil, Plant, Environmental and Animal Production Sciences, School of Biotechnological Sciences, University of Naples Federico II, Portici, Italy b Department of Biological Sciences, University of Naples Federico II, Naples, Italy

... 1 . 2.2. In silico analysis of cellular localisation. The computational prediction of subcellular localisation of POX A1b in plants was carried out by ProtComp 9.0 (http://www.softberry.com). 2.3. Expression vector construction. The ...

Biologia Plantarum
Volume 55, Issue 4 , pp 625-633 DOI: 10.1007/s10535-011-0160-1

Characterization and expression analysis of the SNF2 family genes in response to phytohormones and abiotic stresses in rice

X. -Y. Li et al.,
1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Wushan, Guangzhou, 510642, P.R. China

... Subcellular localization of the rice SNF2 proteins was predicted in silico using the programs WOLF PSORT (Horton et al. 2007), ProtComp8.0 (http://linux1. softberry.com/berry.phtml) and NUCLEO (Hawkins et al. 2007). The ...

African Journal of Microbiology Research
Vol. 5(18), pp. 2590-2595, 16 September, 2011 DOI: 10.5897/AJMR11.133

Cloning and characterization of a female gametophyte-specific gene in Gracilaria lemaneiformis (Gracilariales, Rhodophyte)

Peng Chen 1,4, HongBo Shao 1,2* and Di Xu 3
1The CAS/Shandong Provincial Key Laboratory of Coastal Environmental Processes, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences (CAS), Yantai 264003, China. 2Institute for Life Sciences, Qingdao University of Science and Technology (QUST), Qingdao 266042, China.

... org/tools/protparam.html). Protein analysis was performed with ProtComp (www.softberry. com), TMHMM (http://www.cbs.dtu.dk/services/TMHMM-2.0/) and PSORT (http://psort.nibb. ac.jp/form2.html). RESULTS Screening of the SSH cDNA libraries ...

Plant Physiology and Biochemistry
Volume 49, Issue 9, September 2011, Pages 1064–1070 DOI: 10.1016/j.plaphy.2011.07.010,

Characterization of the sulfurtransferase family from Oryza sativa L

Sebastian Guretzki, Jutta Papenbrock
Institute for Botany, Leibniz University Hannover, Herrenhauserstr. 2, D-30419 Hannover, Germany

... number, the length (aa) and the mass (kDa) for 24 Str in Oryza are summarized [PSORT, WoLF PSORT, iPSORT, and TargetP (http://www.expasy.org/tools/); MultiLoc and TargetLoc (http://abi.inf.uni-tuebingen.de/Services/MultiLoc/) ProtComp (http://linux1.softberry.com/berry ...

Reproduction in Domestic Animals
(2011), 46: 980–989. doi: 10.1111/j.1439-0531.2011.01771.x

Molecular Cloning of Sheep and Cashmere Goat Pdia3 and Localization in Sheep Testis.

Lv, L., Ujisguleng, B., Orhontana, B., Lian, W. and Xing, W.
The key laboratory of mammalian reproduction biology and technology of ministry of education, School of Life Sciences, Inner Mongolia University, Hohhot, China

... smart.embl.de/smart/set_mode.cgi?NORMAL=1), InterProScan (http://www.ebi.ac.uk/Tools/pfa/ iprscan/), ExPASy-Compute pI/Mw tool (http://expasy.org/tools/pi_tool.html), ExPASy ScanProsite (http://expasy.org/tools/scanprosite), ProtComp v. 9.0 (http://linux1.softberry.com/berry ...

PLoS ONE
6(8): e23786. (2011) doi:10.1371/journal.pone.0023786

Identifying Schistosoma japonicum Excretory/Secretory Proteins and Their Interactions with Host Immune System.

Liao et al.,
Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China, Key Laboratory for Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou, People's Republic of China, Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, People's Republic of China

...By using the above strategy, the final precision to predict ES proteins was 100% for 8 groups of tested proteins and the average recall is 81.7%, which is much higher than state-of-art methods: SignalP [12], SecretomeP [13], Phobius [22] and ProtComp [23] (Table 1). ...

J. Antimicrob. Chemother.
(2011) 66 (1): 79-85. doi: 10.1093/jac/dkq418

Contribution of CmeG to antibiotic and oxidative stress resistance in Campylobacter jejuni

Byeonghwa Jeon 1,†, Yang Wang 1,2, Haihong Hao 1,3, Yi-Wen Barton 1 and Qijing Zhang 1
1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA 2Department of Pharmacology and Toxicology, College of Veterinary Medicine, China Agricultural University, Beijing, China

...CmeG is predicted to be an inner membrane protein by ProtComp Ver. 3.1 (http://linux1.softberry.com/berry.phtml) (data not shown) and transmembrane domain analysis (http://www.tcdb.org/progs/hydro.php) showed that CmeG possesses 12 TMs (see sequence alignment in Figure S1, available as Supplementary data at JAC Online). ...

Functional Plant Biology
38(6) 479-492 http://dx.doi.org/10.1071/FP10246

Analysis of differentially expressed genes in leaf rust infected bread wheat involving seedling resistance gene Lr28

Dhariwal et al.,
A Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut-250004, UP, India. B Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India.

... Motif and Prosite pattern identification was carried out using PPSearch program (Prosite Database, EMBL-EBI). Locations of proteins in tissue were predicted using ProtComp V. 9.0 program (available at http://www.softberry.com/berry.phtml, accessed 9 June 2009). ...

Genomics and Applied Biology
2011, Vol.2 No.1 doi: 10.5376/gab.2011.02.0001

Cloning of an Ascorbate Peroxidase Gene from Puccinellia tenuiflora and its Expression Analysis

Qingjie Guan 1,2 Lin Li 1 Takano Tetsuo 2 Shenkui Liu 1
1. Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, 150040; 2. Asian Natural Environment Science Center (ANESC), The University of Tokyo, Tokyo, 1880002, Japan

... nph) by ProtParam soft. At last, the subcellular localization of PutAPx gene was analysed and predicted respectively by PSORT and ProtComp Version 611 softwares (http://www.softberry. Compberry.phtml). 3.6 Congstruction of ...

Plant Physiology and Biochemistry
Volume 49, Issue 7, July 2011, Pages 792–799 DOI: 10.1016/j.plaphy.2011.01.018

Molecular cloning, characterization, and expression of an alfalfa (Medicago sativa L.) heme oxygenase-1 gene, MsHO1, which is pro-oxidants-regulated

Fu et al.,
a College of Life Sciences, Cooperative Demonstration Laboratory of Centrifuge Technique, Nanjing Agricultural University, Nanjing 210095, PR China b Institute of Botany, Jiangsu Province and the Chinese Academy of Sciences, Jiangsu Province Key Laboratory for Plant Ex-situ Conservation, Nanjing 210014, PR China

... HY1 in Arabidopsis is most likely localized in the plastids [21] and [22]. In this study, MsHO1 protein was predicted to be located in the mitochondrial, endoplasmic reticulum, and chloroplast by ProComp v9.0 (http:/linux1.softberry.com/berry). ...

Plant Science
Volume 181, Issue 3, September 2011, Pages 242–248 DOI: 10.1016/j.plantsci.2011.05.016,

Cellular localization of dual positional specific maize lipoxygenase-1 in transgenic rice and calcium-mediated membrane association

Cho et al.,
a Department of Molecular Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea b Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea

... v.1.03, SignalP 3.0, TargetP 1.1 and SIGFIND 2. However, none of these programs identified any potential targeting sequence except ProtComp 6.1 which predicted that ZmLOX1 is a cytoplasmic membrane-bound protein with ProtComp score of 11.1 (http://www.softberry.com/). ...

Journal of Theoretical Biology
Volume 262, Issue 4, 21 February 2010, Pages 750-756

Predict potential drug targets from the ion channel proteins based on SVM

Chen Huang et al.,
a College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China b Biomedical Engineering Institute of CUMS, Beijing 100054, China

... In stage 2, we searched for potential ion channel targets based on known ion channel target protein characteristics. 2. Method. 2.1. Datasets. ... The ProtComp 8.0 program (ProtComp) was used to predict protein subcellular localization. ...

Molecular Oncology
Volume 4, Issue 6, Pages 496-510 (December 2010)

Cancer secretomics reveal pathophysiological pathways in cancer molecular oncology

George S. Karagiannis ab, Maria P. Pavlou ab, Eleftherios P. Diamandis abc
a Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada b Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada

... Protcomp algorithms (http://www.softberry.com) [Softberry ProtComp 6.0 [http://www.softberry. com/berry.phtml?topic=protcompan&group=help&subgroup=proloc]], SignalP (http://www.cbs. dtu.dk/services/SignalP/) ([Bendtsen et al., 2004a] and [Bendtsen et al., 2004b]), web ...

Mol Biol Rep.
2010 Feb;37(2):1081-8.

Molecular analysis of an actin gene, CarACT1, from chickpea (Cicer arietinum L.)

Peng et al.,
State Key Laboratory of Crop Genetics and Germplasm, Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, 210095 Nanjing, China

... The putative CarACT1 had 377 amino acids with the pre- dicted molecular mass of 41.96 kD and the isoelectric point of 5.16. Based on the analysis by the Softberry program (ProtComp v8.0; http://linux1.softberry.com/berry.phtml), CarACT1 was localized in the cytoplasm. ... 

BMC Genomics
2010, 11:225doi:10.1186/1471-2164-11-225

Differential transcript expression between the microfilariae of the filarial nematodes, Brugia malayi and B. pahangi

Michael M Kariuki 1, Leonard B Hearne 2 and Brenda T Beerntsen
1 Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA 2 Department of Statistics, College of Arts and Science, University of Missouri, Columbia, MO 65211, USA

... preferentially expressed transcripts were further analyzed by PSORTII [24] and ProtComp (http://www.softberry.com); two protein algorithm that give more detailed protein localization predictions. ... localization algorithm, ProtComp, from Softberry Inc (http://www.softberry.com/). ... 

Appl. Comput. Math.
V.9, Special Issue, 2010, pp. 19-33

POSSIBLE FUNCTIONAL AND EVOLUTIONARY ROLE OF PLASTID DNA INSERTIONS IN RICE GENOME

YAGUT YU. AKBAROVA 1,2, VICTOR V. SOLOVYEV 3, ILHAM A. SHAHMURADOV 1
1 Bioinformatics Laboratory, Institute of Botany, Baku AZ1073, Azerbaijan 2 College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Sultanate of Oman 3 Department of Computer Science, Royal Holloway, University of London, Egham, Surrey TW20, UK

... of amino acid sequences has been carried out by BLAST program [1]. Search for statistically significant open reading frames (ORFs) and putative target compartments of proteins were done by BESTORF and ProtComp programs, respectively (http://www.softberry.com). ... 

Molecular Biotechnology
2010 Volume 44, Number 1, 30-40, DOI: 10.1007/s12033-009-9202-8

Cloning and Characterization of a Novel NAC Family Gene CarNAC1 from Chickpea (Cicer arietinum L.)

Peng et al.,

... CarNAC1 is a Nuclear Protein Transcription factor always functions in the nuclei, and numerous NACs have been located in the cell nucleus [3, 4, 20]. In this study, CarNAC1 was predicted to be located in the nucleus by ProComp v8.0 (http://linux1.softberry.com/ berry). ... 

Planta
2010 Volume 231, Number 6, 1425-1437, DOI: 10.1007/s00425-010-1143-8

Comparative molecular and biochemical characterization of segmentally duplicated 9-lipoxygenase genes ZmLOX4 and ZmLOX5 of maize

Yong-Soon Park, Susan Kunze, Xinzhi Ni, Ivo Feussner and Michael V. Kolomiets
(1) Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132, ETATS-UNIS (2) Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August University, Justus-von-Liebig-Weg 11, 37077 Gottingen, ALLEMAGNE

... Four different pub- licly available programs, including ProtComp (http://linux1. softberry.com), TargetP (http://www.cbs.dtu.dk/services/ TargetP/), ChloroP (http://www.cbs.dtu.dk/services/ ChloroP/) and WolfPsort (http://wolfpsort.org) were utilized to pre- dict the subcellular ...

Biosci Rep.
2009 Oct 9;30(1):59-71, 1 p following 71

Characterization of Citrus sinensis type 1 mitochondrial alternative oxidase and expression analysis in biotic stress

Daurelio LD, Checa SK, Barrio JM, Ottado J, Orellano EG
Molecular Biology Division, IBR (Instituto de Biologia Molecular y Celular de Rosario), CONICET (Consejo Nacional de Investigaciones Cientificas y Tecnicas), Universidad Nacional de Rosario, Suipacha 531, (S2002LRK) Rosario, Argentina.

... services/SignalP/). Subcellular localization was analysed using ProtComp v6.0 (http://www.softberry.com, Protein location/patterns/Epitops, ProtComp) and TargetP (http://www.cbs.dtu.dk/services/TargetP/). Transcription and ... 

Biochimica et Biophysica Acta (BBA) - Bioenergetics
Volume 1787, Issue 3, March 2009, Pages 135-143

Cyanobacterial cytochrome c_M: Probing its role as electron donor for Cu_A of cytochrome c oxidase

Bernroitner et al.,
aMetalloprotein Research Group, Division of Biochemistry, Department of Chemistry, BOKU – University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna, Austria

... role as either signal peptide or transmembrane helix several bioinformatic tools were used (selected organism group: gram negative prokaryotes): (i) SignalP, version 3.0 (http://www.cbs. dtu.dk/services/SignalP/) [30]; (ii) ProtCompB, version 3 (http://www.softberry.com/berry ...

Biosci Rep.
2009 Oct 9;30(1):59-71, 1 p following 71

Characterization of Citrus sinensis type 1 mitochondrial alternative oxidase and expression analysis in biotic stress

Daurelio LD, Checa SK, Barrio JM, Ottado J, Orellano EG.
Molecular Biology Division, IBR (Instituto de Biologia Molecular y Celular de Rosario), CONICET (Consejo Nacional de Investigaciones Cientificas y Tecnicas), Universidad Nacional de Rosario, Suipacha 531, (S2002LRK) Rosario, Argentina

... Subcellular localization was analysed using ProtComp v6.0 (http://www.softberry.com, Protein location/patterns/Epitops, ProtComp) and TargetP (http://www.cbs.dtu.dk/services/TargetP/). Transcription and translation initiation sites were inferred with ProScan ...

Plant Physiology and Biochemistry
Volume 47, Issues 11-12, November-December 2009, Pages 1037-1045

Characterization of a chickpea (Cicer arietinum L.) NAC family gene, CarNAC5, which is both developmentally- and stress-regulated

Hui Peng et al.,
aState Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China bKey Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin 541004, China

... View Within Article. 2.4. CarNAC5 is a nuclear protein. Numerous NACs have been located in the nucleus [5], [6] and [18]. In this study, CarNAC5 protein was predicted to be located in the nucleus by ProtComp v8.0 (http://linux1.softberry.com/berry). ...

Current Genetics
Volume 55, Number 4 / August 2009 ,pp. 485-496

Functional analysis of an a-1,2-mannosidase from Magnaporthe oryzae

Jie Zhou et al.,
(1) The Ministry of Education Key Laboratory of Biopesticide and Chemical Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China (2) Department of Plant Pathology and Microbiology, Texas A & M University, College Station, TX 77843-2132, USA

... al. 2004), and SignalP 3.0 (http://www.cbs.dtu.dk/services/) (Nielsen et al. 1997) and Protcomp v8.0 (Softberry.com) were applied to predict its cleavage site and its possible sub-cellular localiza- tion (Soderlund et al. 2006). The ...

Infection and Immunity
October 2009, p. 4356-4361, Vol. 77, No. 10 doi:10.1128/IAI.00242-09

High-Throughput Identification of New Protective Antigens from a Yersinia pestis Live Vaccine by Enzyme-Linked Immunospot Assay{triangledown}

Bei Li et al.,
Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing 100071, China,1 Yunyang Medical College, Shiyan, Hubei Province, China2

... were subjected to computer analysis to identify genes potentially encoding surface-exposed, membrane-associated proteins by using PSORTb (http://www.psort.org/psortb/), SignalP (http://www.cbs.dtu.dk/services/SignalP/), and ProtcompB (http://linux1.softberry.com/berry.phtml ...

Plant Physiology Preview
Published on September 16, 2009; 10.1104/pp.109.144766

A Nuclear Factor Regulates Abscisic Acid Responses in Arabidopsis

Min Jung Kim , Ryoung Shin , and Daniel P. Schachtman
Donald Danforth Plant Science Center, St. Louis, MO 63132

... npx1-1 and wild type. NPX1 Is a Nuclear Protein We identified three putative nuclear localization sequences (NLS; softberry ProtComp6.0 http://www.softberry.com/berry. phtml?topic=protcompan&group=help& sub group =proloc ...

New Phytologist,
2008 Volume 177 Issue 1, Pages 77 - 89

Transcript profiles of the cytokinin response regulator gene family in Populus imply diverse roles in plant development

Gustavo A. Ramirez-Carvajal, Alison M. Morse and John M. Davis
1 Plant Molecular and Cellular Biology Program, University of Florida, PO Box 110690, Gainesville, FL 32611, USA; 2 School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL 32611, USA

... silico using the software packages TargetP1.1 (http://www.cbs.dtu.dk), WoLF PSORT (http://www.wolfpsort.seq.cbrc.jp) and ProtComp 6.0 (http://www.softberry.com ...

Current Genetics
Volume 53, Number 4 / April, 2008 Page 217-224

Biochemical and molecular characterization of a putative endoglucanase in Magnaporthe grisea

Jie Zhou et al.,
(1) The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, 350002 Fuzhou, People’s Republic of China (2) The School of Life Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, People’s Republic of China (3) Departmant of Plant Pathology and Microbiology, Texas A & M University, College Station, TX 77843-2132, USA

... cbs.dtu.dk/services/), and it was also predicted as being a secretory protein tar- geted at the extracellular compartment by ProtComp (http:/ /www.softberry.com ...

Planta
Volume 227, Number 2 / January, 2008 Pages 491-503

A novel plastidial lipoxygenase of maize ( Zea mays ) ZmLOX6 encodes for a fatty acid hydroperoxide lyase and is uniquely regulated by phytohormones and pathogen infection

Xiquan Gao, Michael Stumpe, Ivo Feussner and Michael Kolomiets
(1) Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843-2132, USA (2) Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany

... otherwise. Subcellular localization was predicted using four diVer- ent programs ProtComp (http://www.softberry.com/berry. phtml ...

Molecular Genetics and Genomics
Volume 279, Number 1 / January 2008 27-39

Identification and characterization of secreted and pathogenesis-related proteins in Ustilago maydis

Olaf Muller, Peter H. Schreier and Joachim F. Uhrig
(1) Max Planck Institute for Plant Breeding Research, Carl-von-Linne' Weg 10, 50829 Koeln, Germany (2) Present address: Department of Regine Kahmann, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany

... ProtComp (v. 6.0; http://www.soft- berry.com) analyzes the entire protein sequence ... neu- ral network, NN, and hidden markov model, HM) and prot- comp (v. 6.0 ...

MPMI
December 2008, Volume 21, Number 12 Pages 1571-1581

Phases of Infection and Gene Expression of Fusarium graminearum During Crown Rot Disease of Wheat

Amber E. Stephens, Donald M. Gardiner, Rosemary G. White, Alan L. Munn, and John M. Manners
1CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Brisbane, QLD 4067, Australia; 2The Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia 3CSIRO Plant Industry, PO Box 1600, Canberra ACT 2601, Australia

.. Of these, 19 are predicted to be extracellular secreted proteins (ProtComp 6.0; Softberry, Inc., Mount Kisco, NY, USA) and most, if not all, probably act as ...

Eukaryotic Cell
February 2008, p. 368-378, Vol. 7, No. 2

A Botrytis cinerea Emopamil Binding Domain Protein, Required for Full Virulence, Belongs to a Eukaryotic Superfamily Which Has Expanded in Euascomycetes

Gioti et al.
UMR1290 BIOGER-CPP, INRA, Route de St-Cyr, 78026 Versailles, France

... 4). BcPIE3 protein was predicted to locate at the endoplasmic reticulum membrane according to Protcomp version 6.0 software (http://www.softberry.com). ...

PLoS ONE.
2008; 3(6): e2300.

Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis

Darren M. Soanes et al.,
1School of Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom 2School of Computer Science, University of Manchester, Manchester, United Kingdom

... For example, a similar analysis for M. grisea using SignalP and ProtComp (www.Softberry.com) predicted only 739 secreted proteins (out of a proteome of 11,109 ...

Insect Biochemistry and Molecular Biology
Volume 38, Issue 2, February 2008, Pages 166-175

Angiotensin-converting enzyme in Spodoptera littoralis: Molecular characterization, expression and activity profile during development

Els Lemeire, Bartel Vanholme, Thomas Van Leeuwen, John Van Camp and Guy Smagghe
Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium bResearch Group of Applied Molecular Genetics, Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium cResearch Group of Food Chemistry and Human Nutrition, Department of Food Safety and Food Quality, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium

... Server (Nielsen et al., 1997; Bendtsen et al., 2004) and sub-cellular localization of the protein was predicted by Protcomp 6.0 (http://sun1.softberry.com/berry ...

Experimental Parasitology ,
Volume 117, Issue 2, October 2007, Pages 124-132

Toxocara canis: Molecular cloning, characterization, expression and comparison of the kinetics of cDNA-derived arginine kinase

Susiji Wickramasinghe et al.,
Department of Environmental Health Sciences, Kochi Medical School, Oko, Nankoku City, Kochi 783-8505, Japan

...... i Softberry (http://sun1.softberry.com/cgi-bin/programs/proloc/protcompan.pl). j ...

Trends in Plant Science ,
Volume 12, Issue 6, June 2007, Pages 239-244

The tify family previously known as ZIM

Bartel Vanholme, Wim Grunewald, Alex Bateman, Takayuki Kohchi and Godelieve Gheysen
Faculty of Bioscience Engineering, Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
2Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
3Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan

...Subcellular localization as predicted by Protcomp 6.0 from Softberry. d ...

Nature Protocols,
2, 953 - 971 (01 Apr 2007)

Locating proteins in the cell using TargetP, SignalP and related tools

Olof Emanuelsson, SA,ren Brunak, Gunnar von Heijne, Henrik Nielsen

...SignalP 3.0, SignalP 2.0 and TargetP to PrediSi, Phobius and ProtComp 6.0 (a commercially available program from Softberry Inc.) on a set of exclusively mammalian proteins....

Journal of Biochemistry and Molecular Biology,
Vol. 40, No. 2, March 2007, pp. 247-260

Molecular Cloning of Two Genes Encoding Cinnamate 4-Hydroxylase (C4H) from Oilseed Rape (Brassica napus)

An-He Chen 1,2,, You-Rong Chai 1,, Jia-Na Li 1,,* and Li Chen 1
1Chongqing Rapeseed Technology Research Center; Chongqing Key Laboratory of Crop Quality Improvement; Key Lab of Biotechnology & Crop Quality Improvement of Ministry of Agriculture; College of Agronomy and Life Sciences, Southwest University, Beibei, Chongqing 400716, People’s Republic of China
2College of Bio-Information, Chongqing University of Posts and Telecommunications, Huang jueya, Nanan Zone, Chongqing 400065, People’s Republic of China

...respectively. Softberry- ProtComp 6.0 (http://www.softberry. com/berry.phtml) also definitely predicted them to be ER-membrane bound with scores of 3.1 and 3.0 respectively...

Journal of Experimental Botany
2006 57(14):3767-3779; doi:10.1093/jxb/erl137

Duplicate maize 13-lipoxygenase genes are differentially regulated by circadian rhythm, cold stress, wounding, pathogen infection, and hormonal treatments

Andriy Nemchenko1, Susan Kunze2, Ivo Feussner2 and Michael Kolomiets1,*
1Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132, USA
2Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August University Gottingen, Justus-von-Liebig-Weg 11, D-37077 Gottingen, Germany

... Subcellular localization was predicted based on the identification of signal peptide sequences by four different programs ProtComp (www.softberry.com/berry ...

NATURE
444, 97-101 (2 November 2006)

Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

Jorg Kamper et al.,
Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse, D-35043 Marburg, Germany

...Prediction of secreted proteins. For the prediction of amino-terminal secretion signals, SignalP 3.0 (ref. 26) was used. A total of 750 proteins were predicted to carry a signal peptide both by the hidden Markov and the neural network algorithms. These candidates were analysed with the integral prediction score of ProtComp 6.0 (http://www.softberry.com), yielding 426 candidate secreted proteins. ...

In Silico Biology
7, 0002 (2006)

In silico analysis of the Lateral Organ Junction (loj) gene and promoter of Arabidopsis thaliana

Dipnarayan Saha et al.,
National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India

The probable organelle targeting signal sequence was detected using TargetP 1.1 (http://www.cbs.dtu.dk/services/TargetP/) [Emanuelsson et al., 2000], Mitoprot v1.0a4 (http://ihg.gsf.de/ihg/mitoprot.html) [Claros and Vincens, 1996], Predotar v1.03 (http://urgi.infobiogen.fr/predotar/) [Small et al., 2004], ProtComp v6.0 (SoftBerry Inc.) (http://www.softberry.com/) and Plant RNA Binding Protein Database (PlantRBP) (http://plantrbp.uoregon.edu/advsearch.php).

MPMI (Molecular plant-microbe interactions)
Vol. 19, No. 10, 2006, pp. 1055-1061 DOI: 10.1094/MPMI -19-1055.

TECHNICAL ADVANCE
MGOS: A Resource for Studying Magnaporthe grisea and Oryza sativa Interactions

Carol Soderlund et al.,
Arizona Genomics Computational Laboratory, Bio5 Institute, University of Arizona, Tucson 85721, U.S.A

Hence, the ESTs and genomic sequence for M. grisea were mined for putatively secreted proteins using SignalP (Bendtsen et al. 2004) to identify those containing likely signal sequence cleavage sites and PROTCOMP, available from Softberry, to predict cellular localization of the putative proteins, which resulted in 739 proteins.

Molecular Biology Reports
33 (2006), 4, 279-285

GmZFP1 encoding a single zinc finger protein is expressed with enhancement in reproductive organs and late seed development in soybean (Glycine max)

Fang Huang, Yingjun Chi, Qingchang Meng, Junyi Gai and Deyue Yu
National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

... the ProtComp program (http://. www.softberry.com) still predicted that GmZFP1 pro- ..

Nucleic Acids Research
2006, Vol. 34, No. 17 4685-4701 doi:10.1093/nar/gkl588

Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae

Cathryn Rehmeyer et al.,
Department of Plant Pathology and 2Department of Biology, University of Kentucky, Lexington, KY 40546 USA

Cellular localization prediction for secreted proteins was performed with ProtComp version 6.0 for animal and fungi (www.softberry.com).

GENES & DEVELOPMENT
(2006) 20:1365-1377

The chicken talpid3 gene encodes a novel protein essential for Hedgehog signaling

Megan G. Davey et al.,
Division of Cell and Developmental Biology, Wellcome Trust Biocentre (WTB), University of Dundee, Dundee DD1 5EH, United Kingdom

Using the program ProtComp, the KIAA0586 protein was predicted to be cytoplasmic.

DNA Sequence - The Journal of Sequencing and Mapping
Volume 17, Number 1 / February 2006 pp. 41 - 48

Molecular cloning and characterization of a rice blast-inducible RING-H2 type Zinc finger gene

Xiang-Bing Meng, Wen-Sheng Zhao, Rui-Ming Lin, Min Wang, You-Liang Peng
China Agricultural University, Department of Plant Pathology, Beijing, 100094, People's Republic of China

... were identified in putative OsRING-1 protein. The ProtComp program (http://softberry. com) a putative nuclear localization motif ...

Journal of Lipid Research
, Vol. 47, 268-283, February 2006

Further characterization of mammalian ceramide kinase: substrate delivery and (stereo)specificity, tissue distribution, and subcellular localization studies

Helena Van Overloop, Sofie Gijsbers, and Paul P. Van Veldhoven
Katholieke Universiteit Leuven, Faculteit Geneeskunde, Departement Moleculaire Celbiologie, Afdeling Farmacologie, Leuven, Belgium

... as predicted by different algorithms [SignalP 3.0 (54), http://www.cbs.dtu.dk/services/ SignalP/#submission; ProtComp 6.0, http://sun1.softberry.com/berry.phtml ...

Microbiology
152 (2006), 547-554

MfLIP1, a gene encoding an extracellular lipase of the lipid-dependent fungus Malassezia furfur

Sascha Brunke and Bernhard Hube
Robert Koch-Institut, Nordufer 20, D-13353, Berlin, Germany

... 2.0 algorithm (Krogh et al., 2001 ) and TargetP 1.1 (Emanuelsson et al., 2000 ) at the CBS prediction server, or with ProtComp 6.0 at www.softberry.com, with ...

Genes and Immunity,
2005, 6, 319–331. doi:10.1038/sj.gene.6364173

Immune response in silico(IRIS): immune-specific genes identified from a compendium of microarray ...

AR Abbas, D Baldwin, Y Ma, W Ouyang, A Gurney, F ...
Department of Bioinformatics, Genentech, Inc., South San Francisco, CA, USA

... The ProtCompalgorithm (Softberry, Inc.) predicts for the 1589 IRIS genes with ORFs that 24% of the encoded proteins are in the plasma membrane, 13% are ...

Plant Molecular Biology
Volume 59, Number 2 / September, 2005, pp. 323-343

Genomic Analysis of the 12-oxo-phytodienoic Acid Reductase Gene Family of Zea mays

Zhang et al.,
1) Department of Plant Pathology and Microbiology, Department of Plant Pathology, Texas A&M University, 2132 TAMU, College Station, Texas 77843-2132, USA (2) Pioneer Hi-Bred International, Inc., 7250 NW 62nd Ave., Johnston, Iowa 50131-0552, USA

... nibb. ac.jp/), TargetP (http://www.cbs.dtu.dk/services/ TargetP/) and ProtComp (http://www.softberry. com/berry.phtml). Transcription ...

BMC Bioinformatics
2005, 6:256doi:10.1186/1471-2105-6-256

Evaluating eukaryotic secreted protein prediction

Eric W Klee and Lynda BM Ellis
Department of Laboratory Medicine and Pathology, University of Minnesota, Mayo Mail Code 609, 420 SE Delaware Street, Minneapolis, MN 55455, USA

... ProtComp 6.0, from Softberry, Inc., predicts protein localization, including extracellular proteins, using a combination of neural networks and sequence ...

Genetics and Molecular Biology
28, 3 (suppl), 529-538 (2005)

Multigene families encode the major enzymes of antioxidant metabolism in Eucalyptus grandis L

Felipe Karam Teixeira, Larissa Menezes-Benavente, Vinícius Costa Galvão and Marcia Margis-Pinheiro
Universidade Federal do Rio de Janeiro, Departamento de Genética, Laboratório de Genética Molecular Vegetal, Rio de Janeiro, RJ, Brazil.

.. Protein sorting and subcellular localization predictions were performed according to ProtComp program Version 5 (http://www.softberry.com/) ...

MPMI
Vol. 17, No. 7, 2004, pp. 789-797. Publication no. M-2004-0426-01R. © 2004 The American Phytopathological Society

Lotus japonicus LjKUP Is Induced Late During Nodule Development and Encodes a Potassium Transporter of the Plasma Membrane

Guilhem Desbrosses, Claudia Kopka, Thomas Ott, and Michael K. Udvardi
Max Planck Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Golm, Germany

...Both PSORT and ProtComppredicted a PM location for LjKUP...

Planta
Issue: Volume 218, Number 6 Date: April 2004 Pages: 965 - 975

Biochemical and immunological characterization of pea nuclear intermediate filament proteins

Sonal S. D. Blumenthal1, Gregory B. Clark1 and Stanley J. Roux1
(1) School of Biological Sciences, Section of Molecular Cell and Developmental Biology, The University of Texas, Austin, TX 78712, USA Stanley J. Roux Email: sroux@uts.cc.utexas.edu

... html), BCM Search Launcher (Protein structure prediction, http:// searchlauncher. bcm.tmc.edu/), SoftBerry (Protein subcellular. localization ...

Comparative and Functional Genomics
Volume 5, Issue 4 , Pages 342 - 353
Published Online: 20 May 2004

Research Paper
Investigation into the use of C- and N-terminal GFP fusion proteins for subcellular localization studies using reverse transfection microarrays
Ella Palmer, Tom Freeman *
MRC Rosalind Franklin Centre for Genomics Research (formerly the HGMP-Resource Centre), Genome Campus, Hinxton, Cambridge CB10 1SB, UK

... ProtCompversion 4 (Softberry) combines results with proteins of known subcellular localization and assumed subcellular localization (based on theoret- ical ...

Plant Physiol.
2004; 134: 286-295.

RHM2 Is Involved in Mucilage Pectin Synthesis and Is Required for the Development...

Usadel et al.

... Tentative subcellular localization prediction by TargetP (Emanuelsson et al., 2000 ) or ProtComp (http://www.softberry.com), a prediction software trained on ...

Journal of Cellular Biochemistry
Volume 90, Issue 2 , Pages 361 - 378
Published Online: 3 Sep 2003

A proteomic study of the arabidopsis nuclear matrix

Tomasz T. Calikowski 1 3, Tea Meulia 2, Iris Meier 1 *
1Department of Plant Biology and Plant Biotechnology Center, Ohio State University, Columbus, Ohio 43210

... For prediction of subcellular localization, ProtComp4 (Softberry, Inc., Mount Kisco, NY; http://www.softberry.com/berry.phtml?topic? proteinloc), PSORT v.6.4 ...

International Journal for Parasitology
Volume 33, Issue 11, 30 September 2003, Pages 1195-1206

Trehalose metabolism genes in Caenorhabditis elegans and filarial nematodes

Pellerone et al.,
a School of Biochemistry & Molecular Biology, Faculty of Science, Australian National University, Canberra, ACT 0200, Australia

... potential GPI anchors, membrane-spanning regions, signal peptides and predicted subcellular localisation using ProtComp ver.5 at http://www.softberry.com/berry ...

The Journal of Neuroscience
August 13, 2003, 23(19):7415-7425

Freud-1: A Neuronal Calcium-Regulated Repressor of the 5-HT1A Receptor Gene

Xiao-Ming Ou et al.,
Ottawa Health Research Institute, Neuroscience, University of Ottawa, Ottawa, Ontario, Canada K1H-8M5

... a consensus nuclear localization signal was not identified, Freud-1 localization is predicted to be nuclear (ProtComp program; http://www.softberry.com/berry ...

Cellular Molecular Life Sciences,
2003, in press

Automatic prediction of protein function

Burkhard Rost 1, 2, 3, *, Jinfeng Liu 1, 3, 4, Rajesh Nair 1, 5, Kazimierz O. Wrzeszczynski 1 and Yanay Ofran 1,6
1 CUBIC, Dept. of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA

... genome/localize/. ProtComp, predict localization for plants, http://www.softberry.com/berry.phtml?topic=proteinloc. Predotar, predict ...

Genome Research
13:2265-2270, 2003

The Secreted Protein Discovery Initiative (SPDI), a Large-Scale Effort to Identify Novel Human Secreted and Transmembrane Proteins: A Bioinformatics Assessment

Hilary F. Clark1, et al.
Departments of Bioinformatics, Molecular Biology and Protein Chemistry, Genentech, Inc., South San Francisco, California 94080, USA

An automated computational strategy was utilized to query each protein translation with the Signal Sensor, Sighmm, Tmdetect (T. Wu, unpubl.), hmmpfam (Eddy 1998 ), and ProtComp (Softberry, Inc.) algorithms. ...The ProtCompalgorithm predicts the subcellular localization of a protein, on the basis of homology to well-annotated proteins, a neural net, and various protein motifs. .. In this case, the ProtCompsubcellular localization prediction was used to categorize these genes as "Other Secreted", "Other Transmembrane", or "Other Cytoplasmic or Nuclear".

Plant Physiol,
February 2002, Vol. 128, pp. 336-340

Gene prediction in eukaryota

Samuel P. Hazen, John S. Scott-Craig, and Jonathan D. Walton*
Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824

... genome/localize/. ProtComp, predict localization for plants, http://www. softberry.com/berry.phtml?topic=proteinloc. Predotar, predict ...

Proc Natl Acad Sci U S A.
2001 April 24; 98(9): 5341-5346.

The Cia5 gene controls formation of the carbon concentrating mechanism in Chlamydomonas reinhardtii

Youbin Xiang, Jun Zhang, and Donald P. Weeks*
Department of Biochemistry and School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0664

...Computer-assisted analysis of the CIA5 aa sequence (PROTCOMP, version 4, http://www.softberry.com) predicted a nuclear localization of the protein.
...Finally, computer program predictions (e.g., PROTCOMP version 4, http://www.softberry.com) for a nuclear localization of CIA5 and the clear-cut nuclear localization of CIA5 in onion epidermal cells (Fig. 3) provide additional weight to the argument that CIA5 may be a transcription factor.

DNA and Cell Biology
2016 doi: 10.1089/dna.2015.3033

Focal Adhesion Kinase Directly Interacts with TSC2 Through its FAT Domain and Regulates Cell Proliferation in Cashmere Goat Fetal Fibroblasts.

Zheng, X. et al.,
1College of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China. 2Hulunbeier Municipal people's Hospital, Hailaer, People's Republic of China. 3Department of Oncology, Kailuan General Hospital, Tangshan, People's Republic of Chian.

... Protein prosite pattern analysis was identified by the Psite program (www.softberry.com). ...

Fish physiology and biochemistry
2016, 1-14. DOI: 10.1007/s10695-016-0238-y

Characterization, promoter analysis and expression of the interleukin-6 gene in blunt snout bream, Megalobrama amblycephala

Fu, X. et al.,
College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural UniversityFreshwater Aquaculture Collaborative Innovation Center of Hubei Province

... Posttranslational modifications were analyzed using SoftBerry-Psite (http://?linux1.?softberry. ?com/?berry.?phtml??topic=?psite&?group=?programs&?subgroup=?proloc) and Motif-Scan (http://?myhits.?isb-sib.?ch/?cgi-bin/?motif_?scan). ...

International journal of molecular sciences
2015, 16(7), 16440-16453. doi:10.3390/ijms160716440

Inhibition of Mammalian Target of Rapamycin Complex 1 (mTORC1) Downregulates ELOVL1 Gene Expression and Fatty Acid Synthesis in Goat Fetal Fibroblasts

Wang, W. et al.,
1 College of Life Sciences, Inner Mongolia University, Hohhot 010021, China 2 College of Basic Medical Science, Inner Mongolia Medical University, Hohhot 010110, China

... Microbody C-terminal targeting signals are boxed. All sites were determined using Psite (Available online: http://www.softberry.com). ... Microbody C-terminal targeting signals are boxed. All sites were determined using Psite (Available online: http://www.softberry.com). ...

Asian-Australasian Journal of Animal Sciences (AJAS)
2013; 26(8): 1057-1064. DOI:10.5713/ajas.2012.12710

Molecular Characterization and Expression Analysis of S6K1 in Cashmere Goats (Capra hircus)

Manlin et al.,
College of Life Science, Inner Mongolia University, Hohhot, 010021, China

.... Protein domains were analyzed using the SMART program (http://smart.embl-heidelberg. de/). Protein prosite patterns were identified using Psite (http://www.softberry.com). ... All sites were determined using Psite (http://www.softberry.com). Figure 2. ...

Asian-Australasian Journal of Animal Sciences (AJAS)
2013; 26(11): 1644-1650. DOI: http://dx.doi.org/10.5713/ajas.2013.13157

Molecular Characterization and Expression Analysis of Ribosomal Protein S6 Gene in the Cashmere Goat (Capra hircus)

Wenlei et al.,
College of Life Science, Inner Mongolia University, Hohhot 010021, China

... isoelectric.ovh.org/. Protein domain analysis was identified by the SMART program (http://smart.embl-heidelberg.de/). Protein prosite patterns analysis were identified by the Psite program (http://www.softberry.com). The model of ...

Asian-Aust. J. Anim. Sci.
Vol. 25, No. 5 : 606 - 612 May 2012 http://dx.doi.org/10.5713/ajas.2011.11290

Molecular Characterization and Expression Pattern of Gene IGFBP-5 in the Cashmere Goat (Capra hircus)

X. J. Wang 1, a et al.,
1 College of Life Science, Inner Mongolia University, The Key Laboratory of Mammal Reproductive Biology and Biotechnology, Ministry of Education, Hohhot 010021, China

... Protein prosite patterns were identified by the Psite program (http://www.softberry.com). A phylogenetic tree was constructed by using the MEGA 4.1 program. RESULTS ... All these were determined using the Psite program (http://www.softberry.com). ...

Asian-Aust. J. Anim. Sci.
June 2012 Vol. 25, No. 6 : 758 - 763 http://dx.doi.org/10.5713/ajas.2011.11398

Molecular Characterization and Tissue-specific Expression of a Novel FKBP38 Gene in the Cashmere Goat (Capra hircus)

X. Zheng et al.,
1 College of Life Science, Inner Mongolia University, The Key Laboratory of Mammal Reproductive Biology and Biotechnology, Ministry of Education, Hohhot 010021, China

... Protein prosite patterns analysis was identified by the Psite program (http://www.softberry.com). The bands on gel were analyzed by Carestream MI software Page 3. Zheng et al. (2012) Asian-Aust. ... All these were determined using the Psite software (http://www.softberry.com). ...

DNA Cell Biol.
2012 May;31(5):839-44. Epub 2011 Dec 16.

Molecular characterization and functional analysis of Cashmere goat mammalian target of rapamycin

Liang Y et al.,
College of Life Science, Inner Mongolia University , The Key Laboratory of Mammal Reproductive Biology and Biotechnology, Ministry of Education, Hohhot, People's Republic of China

... Based on the amino-acid sequence of mTOR, the active sites and domains were predicted using Psite (www.softberry.com) and InterProScan (www.ebi.ac.uk), respectively. ... All sites were determined using Psite (www.softberry.com). ...

Agricultural Sciences in China
Volume 10, Issue 9, September 2011, Pages 1452–1458 DOI: 10.1016/S1671-2927(11)60138-7

Molecular Characterization and Expression Pattern of Rheb Gene in Inner Mongolia Cashmere Goat (Capra hircus)

Xu ZHENG et al.,
College of Life Science, Inner Mongolia University/Key Laboratory of Mammal Reproductive Biology and Biotechnology, Ministry of Education, Hohhot 010021, P.R. China

... embl-heidelberg.de/) and NCBI CDD program (http:// www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb. cgi). Pro- tein prosite patterns analysis were identified by the Psite program (http://www.softberry. com). ... softberry.com). 1456 ZHENG Xu et al. 2011, CAAS. All rights reserved. ...

Plant Pathology
57(1):92-102, February 2008.

A role for oxidative stress in the Citrus limon/Phoma tracheiphila interaction.

Reverberi, M et al.,
... NSite and cellular localization predictions were performed by the software PSITE (© Softberry, Inc. 2000-2005). Statistics TOP. ...

Advanced Materials Research
2013, 647, 304-309 DOI: 10.4028/www.scientific.net/AMR.647.304

Bioinformatics Analysis of OmpA/MotB Protein Encoded by OmpA/MotB Gene(ORF 648bp) of Riemerella anatipestifer

Xu Pan et al.,

... Predicting AntigenicPeptides[17] (http://www.cbs.dtu.dk/services/BepiPred/), ProtScal[18] (http://www.expasy.org/cgi-bin/protscale.pl), CTL epitope-Finder 1.1 (http://linux1.softberry.com/berry.phtml), PSORTb (http://www.psort.org/psortb/), ...