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The programs usage in Scientific publications FGENESH+
FGENESH++
FGENESH-C
FGENESH-2
FGENESH++C

FGENESH+

Theoretical and Applied Genetics
2016 DOI 10.1007/s00122-016-2708-0

Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes

Y.-M. Jeong et al.,
1 Department of Life Science, The Catholic University of Korea, Bucheon 420?743, Korea 2 Epigenomics Research Center of Genome Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea

... For gene prediction, the genome assembly was premasked for class I and class II transposons using RepeatMasker (http://www.repeatmasker.org) and protein- coding genes were predicted ab initio using Fgenesh+ (http://www.softberry.com), AUGUSTUS (Stanke and ...


Theoretical and Applied Genetics
2016 129: 1357. DOI: 10.1007/s00122-016-2708-0

Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes

Jeong, Y. M. et al.,
Department of Life ScienceThe Catholic University of Korea; Epigenomics Research Center of Genome InstituteKorea Research Institute of Bioscience and Biotechnology

... II transposons using RepeatMasker (http://www.repeatmasker.org) and protein- coding genes were predicted ab initio using Fgenesh+ (http://www.softberry.com), AUGUSTUS ...


BMC Genomics
2016,17:657 DOI: 10.1186/s12864-016-3017-3

Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity

Bedre, R., Mangu, V. R., Srivastava, S., Sanchez, L. E., & Baisakh, N.
School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center; Department of Genetics and Biochemistry, Clemson University

... The positions of the SSRs on open reading frames of the genes were determined by using gene finding software MolQuest (FGENESH+; http://linux1.softberry.com/berry.phtml). ...


Molecular plant pathology
2016 DOI: 10.1111/mpp.12444

Fungal phytopathogens encode functional homologues of plant rapid alkalinisation factor (RALF) peptides

Thynne, E. et al.,
Plant Sciences Division, The Australian National University, Canberra, Australia Evolution, Ecology and Genetics Division, Research School of Biology, The Australian National University, Canberra, Australia Computational Evolution Group, The University of Auckland, Auckland, New Zealand

... 2013; Nemri et al. 2014). Where annotations were not present or were different, the online Softberry server (http://linux1.softberry.com/berry.phtml) was used to predict mRNA and protein sequences using the FGNESH+ prediction algorithm (Solovyev et al., 2006). ...


New Phytologist
2016 DOI: 10.1111/nph.14089

The Argonaute-binding platform of NRPE1 evolves through modulation of intrinsically disordered repeats

Trujillo, J. T., Beilstein, M. A., Mosher, R. A.
The School of Plant Sciences, The University of Arizona, Tucson, AZ, USA

... NRPE1 coding sequence was predicted using Fgenesh+ with A. thaliana or O. sativa protein sequences at http://www.softberry.com (Softberry ...


Biologia Plantarum
2016, 60(2), 279-284. DOI: 10.1007/s10535-016-0595-5

The B-, G-and S-genomic Chi genes in family Triticeae

Shoeva, O. Y., Dobrovolskaya, O. B., Leonova, I. N., Salina, E. A., Khlestkina, E. K.
1. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia 2. Food Security Research Center, Novosibirsk State University, Novosibirsk, 630090, Russia

... The gene structure was determined with the FGENESH + program (http://linux1.softberry.com/ berry.phtml, Solovyev 2007). Sequence clustering was performed using the MEGA Page 3. B-, G- AND S-GENOMIC CHI GENES IN TRITICEAE 281 v. 5.1 software (Tamura et al. ...


Theoretical and Applied Genetics
2016, 1-16. DOI 10.1007/s00122-016-2723-1

Fine mapping and identification of candidate genes for the sy-2 locus in a temperature-sensitive chili pepper (Capsicum chinense)

Liu, L. et al.,
1. Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Korea 2. Department of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan

... Gene coding regions of the tomato scaffold were predicted by FGENESH+ (http://linux1.softberry. com). ... repeatmasker.org) and JDotter (http://athena.bioc.uvic.ca). The gene coding regions were predicted with FGENESH (http://linux1.softberry.com) and BLASTX (https://blast. ...


Insect science
2016, 23(3), 366-376. DOI: 10.1111/1744-7917.12333

Genome?wide identification and characterization of odorant?binding protein (OBP) genes in the malaria vector Anopheles sinensis (Diptera: Culicidae)

He, X. et al.,
Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, China

... sinensis genome by TBLASTN with an E-value cut-off at 1E-5. Thereafter, putative OBP sequences were predicted by Fgenesh+ (http://www.softberry.com/). ... sinensis OBP genes were predicted by Fgenesh+ (http://linux1.softberry.com/). ...


BMC plant biology
2015, 15(1), 198. DOI: 10.1186/s12870-015-0550-1

Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic

Marcon, H. S et al.,
Departamento de Genetica, Instituto de Biociencias, Universidade Estadual Paulista – UNESP Programa de Pos-graduacao em Ciencias Biologicas (Genetica), Universidade Estadual Paulista – UNESP

... website. Putative ORFs were retrieved using FGENESH + tool [23] on Softberry platform (http://linux1.softberry.com/berry.phtml) and manually inspected. Conserved domains were annotated using Pfam (http://pfam.xfam.org/). ...


Journal of Molecular Catalysis B: Enzymatic.
Volume 118, August 2015, Pages 79–88. doi:10.1016/j.molcatb.2015.04.010

An unusual feruloyl esterase belonging to family VIII esterases and displaying a broad substrate range

Ohlhoff et al.,
a Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, Cape Town, South Africa b Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa

... BLASTx and BLASTn. The assembled sequences were submitted to FGENESH+ in Softberry (Softberry, Inc., Mount Kisco, NY) for gene prediction and to determine the location of the coding/noncoding regions. The nucleotide ...


Plant Science
2015, Volume 234, May 2015, Pages 50–59, doi:10.1016/j.plantsci.2015.02.005

Modification of plasma membrane NADPH oxidase activity in cucumber seedling roots in response to cadmium stress

Jakubowska, D., Janicka-Russak, M., Kabala, K., Migocka, M., Reda, M.
Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wroclaw, Kanonia Street 6/8, 50-328 Wroclaw, Poland

... homologs of genes encoding NADPH oxidase. Identified sequences were then analyzed using FGENESH and FGENESH+ tools (Softberry, Inc., Mount Kisco, New York; www.softberry.com). ClustalW was used to perform the ...


Eukaryotic cell
2015, 14(2), 158-169 doi: 10.1128/EC.00153-14

Asexual propagation of a virulent clone complex in a human and feline outbreak of sporotrichosis

de Melo Teixeira, M. et al.,
aInstituto de Ciencias Biologicas, Universidade de Brasilia, Brasilia, DF, Brazil bDepartamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Sao Paulo, Sao Paulo, SP, Brazil

... BLASTx and BLASTn. The assembled sequences were submitted to FGENESH+ in Softberry (Softberry, Inc., Mount Kisco, NY) for gene prediction and to determine the location of the coding/noncoding regions. The nucleotide ...


Fungal Genetics and Biology
2014, 62, 55-61. DOI:10.1016/j.fgb.2013.10.013

MAT gene idiomorphs suggest a heterothallic sexual cycle in a predominantly asexual and important pine pathogen

Bihon, W., Wingfield, M. J., Slippers, B., Duong, T. A., Wingfield, B. D.
a Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa b Crop Protection Division, Vegetable and Ornamental Plant Institute, Agricultural Research Council, Private Bag X293, Pretoria 0001, South Africa

... Workbench. Contigs with sequences having high similarity to the M. graminicola MAT1-2-1 sequence were analysed using FGENESH+(http://linux1.softberry.com) and AUGUSTUS (http://augustus.gobics.de) gene prediction programs. ...


Apidologie
2014, 1-15 DOI:10.1007/s13592-014-0292-3

Putative orthologues of genetically identified Drosophila melanogaster chitin producing and organising genes in Apis mellifera

Wang, Y., Odemer, R., Rosenkranz, P., Moussian, B.
1. Animal Genetics, Interfaculty Institute for Cell Biology, Eberhard-Karls University of Tubingen, Auf der Morgenstelle 8, 72076, Tubingen, Germany 2. Apicultural State Institute, University of Hohenheim, August-von-Hartmannstr. 13, 70599, Stuttgart, Germany

... To search for possible exons in the 5? region of GB46725 (coding for the putative grainyhead orthologue), the respective region was scanned manually and by using the software Fgenesh+ (www.?softberry.?com) and Genscan (genes.mit.edu/GENSCAN.html). ...


Plant Pathology
2014 Volume DOI: 10.1111/ppa.12184

Sequence variation in the putative effector gene SIX8 facilitates molecular differentiation of Fusarium oxysporum f. sp. cubense.

Fraser-Smith S. et al.,
1 The University of Queensland, St. Lucia, Qld, Australia 2 Plant Biosecurity Cooperative Research Centre, LPO Box 5012, Bruce, ACT 2617, Australia

... Gene structure was predicted using homology to the Fol-Six8 protein with the program fgenesh+ (Softberry.). ... The amino acid sequence of the Foc-Six8 homologues was predicted using the program fgenesh+ (Softberry) using homology to the Fol-Six8 protein (Fig. ...


Journal of virology
2014, JVI-00209 DOI:

Functional annotation of Cotesia congregata bracovirus: identification of the viral genes expressed in parasitized host immune tissues

Chevignon G. et al.,
1 Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR Sciences et Techniques, universite Francois-Rabelais, Tours, France. 2 Commissariat a l'Energie Atomique et aux energies alternatives, Genoscope (Centre National de Sequencage) Evry, France.

... Whenever overlapping 242 consensus sequences encompassed an entire CDS predicted by FGENESH+ 243 software detection (SoftBerry platform, http://linux1.softberry.com/all.html) on the 244 CcBV integrated genome (14), the corresponding gene was considered to 245 ...


Physiologia plantarum
, 150(1), 32-45. DOI: 10.1111/ppl.12064

Transcriptional regulation of the V?ATPase subunit c and V?PPase isoforms in Cucumis sativus under heavy metal stress

Kabala K. et al.,
Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland

... cucumber sequences were then analyzed using gene finding programs identifying full-length cDNA sequences (comprising the 5? and 3? ends): GeneMark (http://exon.biology.gatech.edu/ eukhmm.cgi) and FGENESH as well as FGENESH+ on the SoftBerry server (http ...


Physiologia Plantarum
Volume 150, Issue 1, pages 32–45, January 2014 DOI:10.1111/ppl.12064

Transcriptional regulation of the V-ATPase subunit c and V-PPase isoforms in Cucumis sativus under heavy metal stress

Katarzyna Kabala*, Malgorzata Janicka-Russak, Malgorzata Reda, Magdalena Migocka
Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland

.. cucumber sequences were then analyzed using gene finding programs identifying full-length cDNA sequences (comprising the 5? and 3? ends): GeneMark (http://exon.biology.gatech.edu/ eukhmm.cgi) and FGENESH as well as FGENESH+ on the SoftBerry server (http ...


Molecular Biology Reports
Volume 40, Issue 4 , pp 2809-2820 DOI:10.1007/s11033-012-2296-2

Isolation and characterization of a Laccase gene potentially involved in proanthocyanidin polymerization in oriental persimmon (Diospyros kaki Thunb.) fruit

Qianni Hu, Chun Luo, Qinglin Zhang, Zhengrong Luo
1. Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Shizishan, Wuhan, 430070, China

... Co., Ltd. Bioinformatics analyses. The similar protein-based gene prediction was performed on the DkLAC1 by the SoftBerry tool (http://linux1.softberry.com/berry.phtml? topic=fgenes_plus&group=programs&subgroup=gfs). The ...


Phil. Trans. R. Soc. B
19 September 2013 vol. 368 no. 1626 20130047 DOI:10.1098/rstb.2013.0047

Functional endogenous viral elements in the genome of the parasitoid wasp Cotesia congregata: insights into the evolutionary dynamics of bracoviruses

Bezier et al.,
1Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Universite Francois Rabelais, Parc de Grandmont, 37200 Tours, France 2Commissariat a l'Energie Atomique, Genoscope (Centre National de Sequencage), 2 rue Gaston Cremieux, CP 5706, 91057 Evry Cedex, France

... For both Cotesia spp., gene predictions were performed using a combination of FGENESH and FGENESH+ software from the SoftBerry platform with the Apis mellifera training set (http://linux1.softberry.com/all.htm) and from the EMBL-EBI platform using Wise2 algorithms (http ...


G3
March 1, 2013 vol. 3 no. 3 465-480 DOI:10.1534/g3.112.004986

Unequal Recombination and Evolution of the Mating-Type (MAT) Loci in the Pathogenic Fungus Grosmannia clavigera and Relatives

Tsui et al.,
*Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4 †Department of Wood Science, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4

... The assembled sequences were submitted to FGENESH+ within Softberry (http://www.softberry. ru/berry.phtml?topic=fgenes_plus&group=programs&subgroup=gfs) for gene prediction and to determine the location of the coding/non coding regions, and manually annotated with ...


Plant and Soil
Volume 364, Issue 1-2 , pp 245-260 DOI:10.1007/s11104-012-1345-x

The genomic organization and transcriptional pattern of genes encoding nitrate transporters 1 (NRT1) in cucumber

M. Migocka, A. Warzybok, G. Klobus
1. Institute of Experimental Biology, Department of Plant Physiology, Wroclaw University, Kanonia 6/8, 50-328, Wroclaw, Poland

... AtNRT1 cDNAs were retrieved from the database and further analyzed using FGENESH and FGENESH+ tools (Softberry, Inc., Mount Kisco, New York; www. ... The structure of each gene was determined using FGENESH or FGENESH+ programs available on softberry.com ...


Plant Pathology
DOI:10.1111/ppa.12184

Sequence variation in the putative effector gene SIX8 facilitates molecular differentiation of Fusarium oxysporum f. sp. cubense

Fraser-Smith et al.,
1The University of Queensland, St. Lucia, Queensland, Australia 2Cooperative Research Centre for National Plant Biosecurity, Australia

... Gene structure was predicted using homology to the Fol-Six8 protein with the software program FGENESH+ (Softberry, Mount Kisco, NY, USA). Nucleotide and amino acid ... program FGENESH+ (Softberry, Mount Kisco, NY, USA) using homology to the Fol-Six8 protein. ...


The FASEB Journal
January 2013 vol. 27 no. 1 86-97 DOI:10.1096/fj.12-219444

Regulation of Anopheles gambiae male accessory gland genes influences postmating response in female

Dottorini et al.,
*Department of Experimental Medicine and †Department of Industrial Engineering, University of Perugia, Perugia, Italy; ‡Department of Biological Sciences, Imperial College London, South Kensington Campus, London, UK; and §Department of Genetics, University of Cambridge, Cambridge, UK

... The full-length sequence, structure, and the multiple variants of the HSF gene were predicted using FGENESH-C, FGENESH+ (http://linux1.softberry.com/), Wise2 (http://www.ebi.ac.uk/), and Genescan (http://genes.mit.edu/GENSCAN.html). Mosquito rearing and mating analysis. ...


Science China Life Sciences
Volume 56, Issue 7 , pp 628-637 DOI:10.1007/s11427-013-4505-1

Cloning and characterization of the gene cluster required for beauvericin biosynthesis in Fusarium proliferatum

Zhang et al.,
14505. CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China 24505. University of Chinese Academy of Sciences, Beijing, 100049, China

... analysis. Gene products of the individual ORFs were deduced and analyzed using the programs AUGUSTUS [18,19] and FGENESH (http://linux1.softberry.com/berry. phtml?topic =fgenes_plus&group=programs&subgroup=gfs). ...


J Phylogen Evolution Biol
Volume 1 • Issue 1 • 1000107 DOI:10.4172/jpgeb.1000107

Ancient Origin of Chaperonin Gene Paralogs Involved in Ciliopathies

Krishanu Mukherjee 1 and Luciano Brocchieri 2*
1Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32610-3610, USA 2Department of Molecular Genetics and Microbiology and Genetics Institute, University of Florida, Gainesville, FL 32610-3610, USA

from the genome and the corresponding query protein was used to guide the prediction of the complete structure of the newly-identified gene, based on homology and on intron-exon junction signals, using the gene-prediction software FGENESH+ [39] at the Softberry web-site (linux1.softberry. com). Reverse


G3
January 1, 2013 vol. 3 no. 1 41-63 doi: 10.1534/g3.112.004044

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

Manning et al.,
*Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 †Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4 ‡Carbone/Ferguson Laboratories, Division of Neuroscience, Oregon National Primate Research Center (ONPRC), Beaverton, Oregon 97006

...Protein-encoding genes were annotated using a combination of manual curation, EST alignments, and ab initio gene predictions made by FGENESH, FGENESH+ (http://linux1.softberry.com) and GENEID (http://genome.crg.es/software/geneid). ...


Fungal Biology
Volume 117, Issue 6, June 2013, Pages 411–421 DOI:10.1016/j.funbio.2013.04.005

Characterization of the mating-type genes in Leptographium procerum and Leptographium profanum

Tuan A. Duong a, Z. Wilhelm de Beer b, Brenda D. Wingfield a, Michael J. Wingfield a
a Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa b Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa

... Plasmids from the positive clones were extracted and inserts were sequenced by primer walking (sequencing primers are available on request). Genes present in the inserts were predicted using FGENESH+ (Salamov and Solovyev 2000) (http://linux1.softberry.com). ...


Gene
Volume 519, Issue 1, 25 April 2013, Pages 18–25 DOI:10.1016/j.gene.2013.01.058

Genome-wide identification and divergent transcriptional expression of StAR-related lipid transfer (START) genes in teleosts

Teng et al.,
a Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China b Graduate University of the Chinese Academy of Sciences, Beijing 100049, China c Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou 325035, China

... Gene predicted using FGENESH+ software (http://linux1.softberry.com/berry.phtml). ... a–?Distinct expression pattern of STARTs suggests divergent functions in development. FGENESH+ software (http://linux1.softberry.com/berry.phtml). ...


PloS one
February 01, 2013DOI: 10.1371/journal.pone.0055185

Genomic and Secretomic Analyses Reveal Unique Features of the Lignocellulolytic Enzyme System of Penicillium decumbens

Liu et al.,
State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

... Gene Finding and Annotation. Gene models were predicted independently with a set of gene finders including Augustus [58], GeneMark-ES [59], GeneId [60] and SoftBerry eukaryotic gene finding suite (Fgenesh and Fgenesh+) [61]. ...


PLoS biology
(2013). 11(6), e1001585. DOI:10.1371/journal.pbio.1001585

Co-Expression of VAL-and TMT-Opsins Uncovers Ancient Photosensory Interneurons and Motorneurons in the Vertebrate Brain

Fischer et al.,
Max F. Perutz Laboratories, University of Vienna, Vienna, Austria, Research Platform “Marine Rhythms of Life,” University of Vienna, Vienna, Austria

...Full-length coding sequences were predicted with FGENESH+ (softberry.com) using Takifugu rubripes TMT-Opsin as input protein sequence. ...


PLoS genetics
(2013). 9(1), e1003233. DOI:10.1371/journal.pgen.1003233

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

Condon et al.,
Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America

... The gene-prediction methods were: EST-based predictions with EST map (http://softberry.com) using raw ESTs and assembled EST contigs for each genome; homology-based predictions with Fgenesh+ [103] and Genewise ....


PLoS Pathog
8(12): e1003037. doi:10.1371/journal.ppat.1003037

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

Ohm et al.,
United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America

... The gene-prediction methods were: EST-based predictions with EST map (http://softberry.com) using raw ESTs and assembled EST contigs for each genome; homology-based predictions with Fgenesh+ [87] and Genewise...


BMC Plant Biology
2012, 12:235 http://www.biomedcentral.com/1471-2229/12/235

Endo-(1,4)-b?-Glucanase gene families in the grasses: temporal and spatial Co-transcription of orthologous genes

Buchanan et al.,
1 Australian Research Council Centre of Excellence in Plant Cell Walls, and the Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, South Australia 5064, Australia. 2 Genetic Discovery Group, Crop Genetics Research and Development, Pioneer Hi-Bred International Inc, 7300 NW 62nd Avenue, Johnston, IA 50131-1004, USA

...and were extracted using the FGENESH + program (Softberry, Inc. 116 Radio Circle, Suite 400Mount Kisco, NY 10549, USA)....


Molecular Reproduction and Development
Volume 79, Issue 6, pages 380–391, June 2012 DOI: 10.1002/mrd.22040

An oocyte-preferential histone mRNA stem-loop-binding protein like is expressed in several mammalian species

Aurore Thelie et al.,
1INRA, UMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, France 2CNRS, UMR7247, Nouzilly, France

... We extracted the syntenic regions in mammals, and then applied several prediction gene methods, including FGENESH+ (http://linux1.softberry.com/berry.phtml), Genscan (Burge and Karlin, 1997), and Genewise (Birney et al., 2004). ...


MPMI
DOI: Vol. 25, No. 2, 2012, pp. 180–190. DOI: 10.1094/ MPMI -08-11-0212

A Highly Conserved Effector in Fusarium oxysporum Is Required for Full Virulence on Arabidopsis

Louise F. Thatcher, Donald M. Gardiner, Kemal Kazan, and John M. Manners
CSIRO Plant Industry, Queensland Bioscience Precinct, St. Lucia, Queensland, 4067, Australia

... gene structure was predicted using homology to F. oxysporum f. sp. lycopersici SIX proteins with FGENESH+ (Softberry, Mount Kisco, NY, U.S.A.), ...


Chemistry & Biology
Volume 19, Issue 12, 21 December 2012, Pages 1611–1619 DOI: 10.1016/j.chembiol.2012.10.010

Terpendole E, a Kinesin Eg5 Inhibitor, Is a Key Biosynthetic Intermediate of Indole-Diterpenes in the Producing Fungus Chaunopycnis alba

Takayuki Motoyama1, Toshiaki Hayashi1, Hiroshi Hirota1, Masashi Ueki1, Hiroyuki Osada1
1 Chemical Biology Core Facility, Chemical Biology Department, RIKEN Advanced Science Institute, Wako-shi, Saitama 351-0198, Japan

... Nucleotide and amino acid sequence data were analyzed by DNASIS-Mac software (Hitachi Software Engineering, Tokyo, Japan). Open reading frames were predicted by FGENESH and FGENESH + software (Softberry, Mount Kiscko, NY). Construction of Recombinant Strains. ...


Fungal Genetics and Biology
Volume 49, Issue 9, September 2012, Pages 708–716 DOI: 10.1016/j.fgb.2012.06.010,

Protein phosphatase Z modulates oxidative stress response in fungi

Leiter et al.,
a Department of Microbial Biotechnology and Cell Biology, Faculty of Science and Technology, University of Debrecen, Egyetem ter 1, H-4032 Debrecen, Hungary b Departament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, Cerdanyola del Valles 08193, Barcelona, Spain

.. 5 2.2. Sequence analysis of fungal PPZ phosphatases DNA sequences were analyzed with FGENESH and FGENESH+ (http://www.softberry.com/berry.phtml; exon-intron analysis), WEBGENE (http://www.itb.cnr.it/sun/webgene; gene structure analysis), pDRAW32 (http://www ...


New Phytologist
Volume 194, Issue 4, pages 1001–1013, June 2012 DOI: 10.1111/j.1469-8137.2012.04128.x

Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

Olson et al.,
1 Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsvag 26, 750 05 Uppsala, Sweden 2 US DOE Joint Genome Institute, Walnut Creek, CA 94598, USA

... based – FGENESH+, Genewise (Birney & Durbin, 2000) seeded by BLASTx (Altschul et al., 1990) alignments against GenBank's database of nonredundant proteins (NR: http://www.ncbi.nlm.nih. gov/BLAST/); and EST-based – EST_map (http://www.softberry.com/) seeded by ...


International Journal of Food Microbiology
Volume 157, Issue 2, 2 July 2012, Pages 202–209 DOI: 10.1016/j.ijfoodmicro.2012.05.008,

The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties

Jure Piskur et al.,
a Wine Research Centre, University of Nova Gorica, Slovenia b Department of Biology, Lund University, Sweden

... 2) homology-based — FGENESH+; Genewise (Birney and Durbin, 2000) seeded by BLASTx alignments against GenBank's database of non-redundant proteins (NR: http://www.ncbi.nlm. nih.gov/BLAST/), and 3) EST-based — EST_map (http://www.softberry.com/) seeded by ...


Fungal Genetics and Biology
Volume 49, Issue 3, March 2012, Pages 217–226 DOI: 10.1016/j.fgb.2012.01.007

The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

Mahajabeen Padamsee et al.,
a Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, United States b Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, United States

... 2) homology-based – FGENESH +; Genewise (Birney and Durbin, 2000) seeded by BLASTx alignments against GenBank's database of non-redundant proteins (NR: http://www.ncbi.nlm. nih.gov/BLAST/), and (3) EST-based – EST_map (http://www.softberry.com/) seeded by ...


African Journal of Biotechnology
Vol. 11 (1), pp. 88-98, 3 January, 2012, DOI: 10.5897/AJB11.3474

Identification and characterization of the Bcl-2-associated athanogene (BAG) protein family in rice

Rashid Mehmood Rana 1, 2, Shinan Dong 1, Zulfiqar Ali 3, Azeem Iqbal Khan 4 and Hong Sheng Zhang 1
1 State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. 2 Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University Rawalpindi, Pakistan.

... The resultant six members of BAG family in rice were processed for further study. Genomic and cDNA sequences of these proteins were retrieved from NCBI and gene structure was predicted by FGENESH+ (http://linux1.softberry.com/berry.phtml). ...


J. Exp. Bot.
(2012) doi: 10.1093/jxb/ers245 First published online: September 20, 2012

Functional analysis of OsHSBP1 and OsHSBP2 revealed their involvement in the heat shock response in rice (Oryza sativa L.)

Rashid Mehmood Rana 1,2, Shinan Dong 1, Haijuan Tang 1, Fiaz Ahmad 1 and Hongsheng Zhang 1
1 State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China 2 Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University Rawalpindi, Pakistan

... by one. The HSBP domain was identified by Pfam (PF06825) to confirm the presence of these proteins in rice. Gene structure was predicted by FGENESH+ (http://linux1.softberry.com/berry.phtml). The chromosomal location ...


Immunogenetics
September 2012 DOI 10.1007/s00251-012-0643-z

Identification of natural killer cell receptor genes in the genome of the marsupial Tasmanian devil (Sarcophilus harrisii)

Lauren E. van der Kraan (1) Emily S. W. Wong (1) Nathan Lo (2) Beata Ujvari (1) Katherine Belov (1)
1. Faculty of Veterinary Science, University of Sydney, B19 RMC Gunn, Sydney, NSW, 2006, Australia 2. School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia

... incomplete, a different gene prediction software, Softberry FGENESH+ (http://linux1.softberry.com/all.htm), was used to re-predict the sequences, incorporating protein homology informa- tion (the BLAST best hit). Functional ...


Gene.
2012 Apr 15;497(2):249-55. Epub 2012 Jan 31.

A novel Acetyl-CoA synthetase short-chain subfamily member 1 (Acss1) gene indicates a dynamic history of paralogue retention and loss in vertebrates.

Castro LF et al.,
University of Porto, Portugal.

... Intron/exon predictions were made with FGENESH+ (http://linux1.softberry.com/berry.138 phtml). 2.2. Phylogenetic analysis. The ACSS1 amino acid sequences retrieved from the genome search were aligned using MAFFT with the L-INS-i method (Katoh and Toh, 2008). ...


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). ...


Plant Physiology October
2011 vol. 157 no. 2 757-769 DOI: 10.1104/pp.111.181990

Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes in Arabidopsis

Guo et al.,
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany

... Gordon et al., 1998). Primer walking and PCR were used to fill or polish gaps and ambiguous regions. Annotation was performed using FGENESH and FGENESH+ (http://linux1.softberry.com/berry.phtml). Spidey (http://www.ncbi ...


Parasitology Research
Volume 108, Issue 3 , pp 611-620 DOI: 10.1007/s00436-010-2104-7

Eimeria maxima phosphatidylinositol 4-phosphate 5-kinase: locus sequencing, characterization, and cross-phylum comparison

Mei-Yen Goh, Mei-Zhen Pan, Damer P. Blake, Kiew-Lian Wan, Beng-Kah Song
1. School of Science, Monash University Sunway Campus, Jalan Lagoon Selatan, 46150 Bandar Sunway, Selangor DE, Malaysia 2. Parasitology, Institute for Animal Health, Compton, Berkshire, RG20 7NN, UK

... Structural annotation of the putative EmPIP5K gene Open reading frame identification was performed by submitting consensus contig sequence to the ab initio gene-prediction programs AUGUSTUS version 2.0.3 (Stanke et al. 2008), FGENESH+ (http://www.softberry. ...


The Journal of Biological Chemistry
March 25, 2011 286, 10419-10428. doi: 10.1074/jbc.M110.179853

Two Novel Classes of Enzymes Are Required for the Biosynthesis of Aurofusarin in Fusarium graminearum

Frandsen et al.,
From the ‡Department of Agriculture and Ecology, Faculty of Life Sciences, University of Copenhagen, DK-1870 Frederiksberg, the §Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby

... default settings (12). Ad hoc ab initio gene modeling was performed using FGENESH and FGENESH+ (SoftBerry). Motifs in unaligned sequences were identified using Meta-MEME version 4.1.1 and MAST (13, 14). Primer design ...


Peptides
Volume 34, Issue 1, March 2012, Pages 193–200

An evolutionary comparison of leucine-rich repeat containing G protein-coupled receptors reveals a novel LGR subtype

Matthias B. Van Hiel a, b, 1, , Hans Peter Vandersmissen a, 1, , Tom Van Loy a, , Jozef Vanden Broeck a
a Animal Physiology and Neurobiology, Zoological Institute of the Katholieke Universiteit Leuven, Naamsestraat 59, P.O. Box 02465, B-3000 Leuven, Belgium b Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Melbourne, Victoria 3010, Australia

... 39, 60]. Possible incorrectly in silico predicted sequences were manually checked at the genomic DNA level and, where possible, repredicted using softberry (http://linux1.softberry.com/berry.phtml) FGENESH+. Sequences were ...


PLoS ONE
6(8): e24111. doi:10.1371/journal.pone.0024111

Topological and Functional Characterization of an Insect Gustatory Receptor

Zhang et al.,
The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing, China CSIRO Food Futures Flagship, Canberra, Australian Capital Territory, Australia

...The genomic scaffold sequences containing candidate genes were predicted using FGENESH+ (http://www.softberry.com/berry.phtml), BGF...


Experimental Parasitology
Volume 127, Issue 1, January 2011, Pages 184–194 DOI: 10.1016/j.exppara.2010.07.012

Identification of papain-like cysteine proteases from the bovine piroplasm Babesia bigemina and evolutionary relationship of piroplasms C1 family of cysteine proteases

Tiago M. Martins a, b, , , Virgilio E. do Rosario b, Ana Domingos a, b
a Unidade de Tecnologias de Proteinas e Anticorpos Monoclonais, Instituto de Higiene e Medicina Tropical, Estrada do Paco do Lumiar 22, 1649-038 Lisboa, Portugal b Centro de Malaria e Doencas Tropicais, Instituto de Higiene e Medicina Tropical, Rua da Junqueira 96, 1349-008 Lisboa, Portugal

... A threshold of E ? 1e-04 was adopted for the tblastn search (Wu et al., 2003). The gene structure of the identified CP genes with multiple exons was predicted using the FGENESH and FGENESH+ software (http://www.softberry.com). ...


J. Exp. Bot.
(2011) 62 (15): 5641-5658. doi: 10.1093/jxb/err249

Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in the FRIGIDA homologue BnaA.FRI.a

Wang et al.,
1Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany 2Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China

... online). The genes were annotated using pairwise sequence alignments (BLAST2; http://www.ncbi.nlm.nih.gov) with FRI and the FGENESH+ and FGENESH_C gene prediction programs (http://linux1.softberry.com/berry.phtml). ...


J. Exp. Bot.
(2011) 62 (10): 3359-3374. doi: 10.1093/jxb/erq321

Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris

Abou-Elwafa et al.,
1Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany 2Broom's Barn Research Centre, Higham, Bury St. Edmunds, Suffolk IP28 6NP, UK

... Beta vulgaris sequences were annotated using pairwise sequence alignments (BLAST2; http://www.ncbi.nlm.nih.gov) against putative A. thaliana orthologues and the FGENESH+ and FGENESH_C gene prediction programs (http://linux1.softberry.com/berry.phtml) for ...


Plant Physiology
February 2011 vol. 155 no. 2 1013-1022 DOI: 10.1104/pp.110.169870

Allelic Variation in the Perennial Ryegrass FLOWERING LOCUS T Gene Is Associated with Changes in Flowering Time across a Range of Populations

Skot et al.,
Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3EB, United Kingdom (L.S., R.S., A.T., K.S., D.T., G.L., I.A.); Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark (T.A.)

... The identity of LpFT3 was confirmed by direct sequencing of the Hd3a.1f/3r-positive BACs with coding sequence and protein prediction generated using FGENESH+ (http://www.softberry.com/ berry.phtml) and by direct comparison with other monocot FT sequences obtained ...


PLoS Pathog
(2011), 7(7): e1002137. doi:10.1371/journal.ppat.1002137

Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens.

Klosterman et al.,
USDA-ARS, Salinas, California, United States of America University of California, Davis, California, United States of America

...Protein-encoding genes were annotated using a combination of manually curated genes, in addition to EST BLAST alignments, and ab initio gene predictions made by FGENESH, FGENESH+ (http://linux1.softberry.com), and ...


PLoS ONE
(2011) 6(8): e22046. doi:10.1371/journal.pone.0022046

Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs.

Zhang et al.,
Department of Biology, University of Padua, Padova, Italy, Abteilung fur Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universitat zu Kiel, Kiel, Germany

...To ensure correct gene structures of all putative GPCR genes, we predicted gene structures using GENSCAN [97], [98] and predictions were repeated using GENOMESCAN [97], [98], GENEWISE [99] and FGENESH/FGENESH+ [31]. Intron-exon structures were determined with the aid of GENEWISE [99] and/or PROT_MAP module of the Softberry software suite (website: www.softberry.org). ...

Nature Biotechnology
29, 922–927 (2011) doi:10.1038/nbt.1976

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris.

Berka et al.,
Novozymes, Inc., Davis, California, USA. US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.

... was performed using ab initio Fgenesh 32 and Genemark-ES 33 ; homology-based Fgenesh+ 32 and Genewise 34 seeded by BLASTx alignments of NCBI's nr (nonredundant) protein database against the assembly; cDNA-based EST_map (http://www.softberry.com/) seeded ...


Insect Molecular Biology
Special Issue: The Aphid Genome
Volume 19, Issue Supplement s2, pages 141–153, March 2010 DOI: 10.1111/j.1365-2583.2009.00975.x

Identification of ion channel genes in the Acyrthosiphon pisum genome

Dale et al.,
1 Syngenta, Jealotts Hill Research Centre, Bracknell, Berkshire, UK; 2 MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, UK;

... eugenes.org/aphid/), was also queried. Softberry protein-based gene predictions software FGENESH+ (http://linux1.softberry.com/berry.phtml) was used to refine gene sequence data. Previously identified members of the Glutamate ... 


Plant Physiology Preview
Published on November 29, 2010; 10.1104/pp.110.169870

Allelic variation in the Lolium perenne L. (perennial ryegrass ) FLOWERING LOCUS T (LpFT3) gene is associated with changes in flowering time across a range of populations

Skot et al.,
1 Aberystwyth University; 2 Aarhus University

... was confirmed by direct sequencing of the Hd3a.1f/3r positive BACs with coding sequence and protein prediction generated using FGENESH+ (http://www.softberry.com/berry.phtml) ... (http://linux1.softberry.com/berry.phtml). Predicted secondary structures for the proteins ...


J. Exp. Bot.
2010 doi: 10.1093/jxb/erq321

Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris

Abou-Elwafa et al.,
1 Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany 2 Broom's Barn Research Centre, Higham, Bury St. Edmunds, Suffolk IP28 6NP, UK

.. Beta vulgaris sequences were annotated using pairwise sequence alignments (BLAST2; http://www.ncbi.nlm.nih.gov) against putative A. thaliana orthologues and the FGENESH+ and FGENESH_C gene prediction programs (http://linux1.softberry.com/berry.phtml) for ...


Experimental Parasitology
Volume 127, Issue 1, January 2011, Pages 184-194 doi:10.1016/j.exppara.2010.07.012

Identification of papain-like cysteine proteases from the bovine piroplasm Babesia bigemina and evolutionary relationship of piroplasms C1 family of cysteine proteases

ATiago M. Martins a, b, Virgilio E. do Rosario b and Ana Domingos a, b
Unidade de Tecnologias de Proteinas e Anticorpos Monoclonais, Instituto de Higiene e Medicina Tropical, Estrada do Paco do Lumiar 22, 1649-038 Lisboa, Portugal b Centro de Malaria e Doencas Tropicais, Instituto de Higiene e Medicina Tropical, Rua da Junqueira 96, 1349-008 Lisboa, Portugal

... A threshold of E 1e-04 was adopted for 93 the tblastn search (Wu et al., 2003). The gene structure of the identified CP genes with 94 multiple exons was predicted using the FGENESH and FGENESH+ software 95 (http://www.softberry.com). ... 


Developmental & Comparative Immunology
Volume 34, Issue 1, January 2010, Pages 1-13 doi:10.1016/j.dci.2009.08.002

Structure and expression pattern of teleost caspase recruitment domain (CARD) containing proteins that are potentially involved in NF-?B signalling

M.X. Chang a, W.Q. Chen a, b and P. Nie a
aState Key Laboratory of Freshwater Ecology and Biotechnology, and Laboratory of Fish Diseases, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, PR China bCollege of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China

... Manual annotation of the orthologous genes was also performed using FGENESH+ to predict structures based on homology with human genes: “fish” specific parameters were applied in this program (http://linux1.softberry.com/berry.phtml). 2.2. Fish and cell line. ... 


Cytokine & Growth Factor Reviews
Volume 20, Issue 2, Pages 115-124

Structural conservation of interferon gamma among vertebrates

R. Savan, S. Ravichandran, J. Collins, M. Sakai, H. Young

... Initially, DYRK2, MDM, RAP1B, NUP107, SLC35E3, CNTN1B, OPN1SW1, CALU harboring scaffolds or contigs were identified. These contigs were then searched for IFN-? gene using FGENESH+ software and curated manually (http://www.softberry.com/berry.phtml). ...


Mol Biol Evol.
2009 May;26(5):1143-53. Epub 2009 Feb 19.

Evolution of mutation rates: phylogenomic analysis of the photolyase/cryptochrome family

Lucas-Lledo JI, Lynch M.
Department of Biology, Indiana University, Bloomington, Indiana, USA.

... The FGENESH+ gene predictor (http://linux1.softberry.com/berry.phtml) was occasionally used to improve the translation of some unannotated eukaryotic genes. Results from different searches were merged and aligned using ClustalX 1.83 (Thompson et al. ...


Mol Biol Evol.
2009 Jul;26(7):1557-69. Epub 2009 Apr 6.

The Fruitless gene in Nasonia displays complex sex-specific splicing and contains new zinc finger domains

Bertossa RC, van de Zande L, Beukeboom LW.
Evolutionary Genetics, Centre for Ecological and Evolutionary Studies, The Netherlands.

... 1990 Go ). In cases in which no or partial sequences were annotated, missing domains were predicted using FGENESH+ at http://linux1.softberry.com/berry.phtml (Solovyev et al. 2006 Go ) using already known protein sequences as template. ...


Genetics.
2009 May;182(1):145-59. Epub 2009 Mar 16.

The multi-AT-hook chromosomal protein of Drosophila melanogaster, D1, is dispensable for viability

Weiler KS.
Department of Biology, West Virginia University, Morgantown, West Virginia 26506, USA

... was identified by tBLASTn of D. simulans genomic sequence using the D. melanogaster protein as a query (http://insects.eugenes.org/species/blast/). FGENESH+ (http://www.softberry.com) was used to predict the partial protein sequence. ...


Science.
2009 May 1;324(5927):626-31.

Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis

Schweitzer et al.,
1 North Carolina State University, Raleigh, NC 27695, USA. 2 North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA.

... two extinct organisms: Mammut americanum (MOR 605) and T. rex (MOR 1125) (see table S1 and SOM appendix) (6). The Anolis carolinensis amino acid sequence was inferred with the use of FGENESH+ (gene prediction on the basis of protein homology; www.softberry.com). ...


BMC Genomics
2009, 10:553 doi:10.1186/1471-2164-10-553

Annotation and expression of carboxylesterases in the silkworm, Bombyx mori

Quan-You Yu 1,2, Cheng Lu *2, Wen-Le Li 2, Zhong-Huai Xiang 2 and Ze Zhang *1,2
1The Institute of Agricultural and Life Sciences, Chongqing University, Chongqing 400044, China and 2The Key Sericultural Laboratory of the Agricultural Ministry of China, Southwest University, Chongqing, 400716, China

... weak sequence similarity to any query sequence and its flanking regions (1 kb or more long) were extracted. Putative COE genes within the extracted sequences were predicted using BGF software [55] and Fgenesh+ (http://www.softberry.com/). Phylogenetic analysis ...


Nature Biotechnology
26, 553 - 560 (2008)

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Diego Martinez et al.,
Los Alamos National Laboratory/Joint Genome Institute, PO Box 1663, Los Alamos, New Mexico 87545, USA. Novozymes, Inc., 1445 Drew Ave., Davis, California 95618, USA.

... an ab initio gene predictor, Fgenesh 37 , specifically trained for this genome, and two homology-based gene predictors, Fgenesh+ (http://www.softberry.com) and ...


Genes & Dev.
2008. 22: 2869-2885 10.1101/gad.1691208

LAB-1 antagonizes the Aurora B kinase in C. elegans

De Carvalho, C. E. et al.,
1Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; 2 Department of Molecular Genetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA

... Prediction of the coding sequence in the respective region in 1003.1 and conceptual translation were performed using FGENESH+ (http://www.softberry.com/berry ...


Nature
Volume 453 Number 7198 pp1064 - 1071 (19 Jun 2008), doi: 10.1038/nature06967

The amphioxus genome and the evolution of the chordate karyotype.

Bowler et al.
# Department of Energy Joint Genome Institute, Walnut Creek California 94598, USA
# Center for Integrative Genomics, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA

... A\Supplementary Note 3. Annotation of protein coding genes 3.1 Expressed sequence tag sequencing. cDNA libraries for amphioxus were prepared from gastrula and neurula stage embryos, and from larvae as described by 6, and a single library was created for Petromyzon marinus (sea lamprey). Approximately 32,000 expressed sequence tags (ESTs) were attempted from each library. (Supplementary Table S6). 3.2 Gene prediction, functional annotation and quality control. The JGI Annotation Pipeline was used for annotation of the amphioxus v1.0 assembly described here. The pipeline includes the following steps: (1) repeat masking, (2) mapping ESTs, full length cDNAs, and putative full length known genes, (3) gene structure prediction using several methods, (4) protein functional annotation using several methods, and (5) combining gene predictions into a non redundant representative set of gene models, which are subject to genome-scale analysis. The genomic sequence, predicted genes and annotations of amphioxus, together with available evidence, are available at the JGI Genome Portal (www.jgi.doe.gov/Amphioxus) and from GenBank under accession number ABEP01000000. Transposons were masked using RepeatMasker 7 tools and a custom library of manually curated repeats (see above Supplementary Note 2.4). 480,070 ESTs were clustered into 77,402 consensus sequences and both individual ESTs and consensus sequences were mapped onto genome assembly using BLAT4. Gene predictors used for annotation of amphioxus v1.0 included ab initio FGENESH 8, homology- based FGENESH+ 8, homology-based GENEWISE 9, and EST-based ESTEXT (Grigoriev, unpublished, available upon request). ...


PLoS ONE.
2008; 3(3): e1889.

Genome-Wide Detection of Serpentine Receptor-Like Proteins in Malaria Parasites

Luciana Madeira et al.,
1Departamento de Parasitologia, Instituto de Ciencias Biome'dicas, Universidade de Sa~o Paulo, Sa~o Paulo, Brasil 2Departamento de Bioqui'mica, Instituto de Qui'mica, Universidade de Sa~o Paulo, Sa~o Paulo, Brasil

... These sequences were submitted to a HMM plus similar protein-based gene prediction using the FGENESH+ program [22] (http://www.softberry.com), setting the ...


Nature
2008, 4doi:10.1038/nature07410

The Phaeodactylum genome reveals the evolutionary history of diatom genomes.

Bowler et al.
1. CNRS UMR8186, Department of Biology, Ecole Normale Supe'rieure, 46 rue d'Ulm, 75005 Paris, France
2. Stazione Zoologica 'Anton Dohrn', Villa Comunale, I-80121 Naples, Italy

... Gene predictors used for these annotations included ab initio Fgenesh 12 trained on sets of known genes and reliable homology-based gene models from P. tricornutum and T.pseudonana, and homology-based Fgenesh+ 12 and Genewise 13 seeded by BLASTX alignments against sequences in the NCBI non-redundant protein set. ...


Nucleic Acids Research
(2007), doi:10.1093/nar/gkm768

ChromDB: The Chromatin Database

Karla Gendler, Tara Paulsen and Carolyn Napoli
BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA

... In many cases, we have derived our own transcript models from genomic sequences using FGNESH or FGENESH+ licensed from Softberry (http://www.softberry.com). ...


BMC Genetics
2008, 9:78 doi:10.1186/1471-2156-9-78

Genomic Complexity of the Variable Region-Containing Chitin-Binding Proteins in Amphioxus

Dishaw et al.,
All Children’s Hospital,Department of Molecular Genetics,801SixthStreet South,St. Petersburg,FL 33701,USA

... html),FGENESH and FGENESH+ (http://linux1.softberry.com/all.htm) or genomescan[63,66] (http://genes.mit.edu/genomescan. html).Details ...


Fish & Shellfish Immunology
Volume 22, Issue 4, April 2007, Pages 351-362

Characterization of an interleukin-15 like (IL-15L) gene from zebrafish (Danio rerio)

I. Gunimaladevi, Ram Savan, Kenji Sato, Ryoji Yamaguchi and Masahiro Sakai
he United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto 1-21-24, Kagoshima, Japan

... 15 gene sequences. The intron-exon structure was determined by FGENESH+ (http://www.softberry.com/berry.phtml). Gene-specific ...


Fungal Genetics and Biology
Volume 44, Issue 2, February 2007, Pages 77-87

Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium

Phil Kersten and Dan Cullen
Forest Products Laboratory, USDA, One Gifford Pinchot Drive, Madison, WI 53705, USA

... Predictions were based on ab initio methods Fgenesh (Salamov and Solovyev, 2000), homology-based methods, Fgenesh+ (www.softberry.com) and Genewise (Birney and ...


J. Biol. Chem.
Vol. 282, Issue 19, 13984-13993, May 11, 2007

Molecular and Functional Characterization of Inositol Trisphosphate Receptors during Early Zebrafish Development

Rachel Ashworth et al.,
School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom

... sequences using the FGENESH+ program, a hidden-Markov model-based algorithm for finding genes with protein similarity, accessible at the Softberry web site. ...


PLoS Biol
(2007) 5(10): e275 doi:10.1371/journal.pbio.0050275

A Novel Snf2 Protein Maintains trans-Generational Regulatory States Established by Paramutation in Maize

Hale CJ, Stonaker JL, Gross SM, Hollick JB
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America

... for CHR156 was identified from BAC CH201-3L17 (GenBank accession AC194602), and gene model prediction was performed using FGENESH+ (Softberry, http: / /www ...


Journal of Molecular Evolution
2007 Volume 65, Number 2 pp. 137-153

Comprehensive Analysis of Animal TALE Homeobox Genes: New Conserved Motifs and Cases of Accelerated Evolution

Krishanu Mukherjee and Thomas R. Burglin
Department of Biosciences and Nutrition, Karolinska Institutet, and School of Life Sciences, Sodertorns Hogskola, Huddinge, Sweden

... carried out with the genomic sequence using the MIT GENSCAN server (http://genes.mit.edu/GENSCAN.html), as well as the FGENESH+ server at Softberry (http://www ...


Genetics
Vol. 176, 599-609, May 2007

The FLOWERING LOCUS T-Like Gene Family in Barley (Hordeum vulgare)

Sebastien Faure, Janet Higgins, Adrian Turner and David A. Laurie
John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom

... New gene predictions were made using FGENESH+ and PROT_MAP (http://sun1.softberry. com) for FT-like genes showing incorrect alignment within the PEBP domain and ...


PNAS
| May 1, 2007 | vol. 104 | no. 18 | 7705-7710

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Brian Palenik et al.,
aScripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202; cJoint Genome Institute and Stanford Human Genome Center, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94304;

... Gene prediction methods used for annotation of two Ostreococcus genomes included ab initio Fgenesh (40), homology-based Fgenesh+ (SoftBerry), Genewise (41 ...


Nature Biotechnology
25, 319 - 326 (2007) Published online: 4 March 2007 | doi:10.1038/nbt1290

Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis

Thomas W Jeffries et al.,
US Department of Agriculture, Forest Service, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, Wisconsin 53705, USA.
Department of Bacteriology, University of Wisconsin-Madison, 420 Henry Mall, Madison, Wisconsin 53706, USA.

... Gene prediction methods used for analysis of the P. stipitis genome include ab initio Fgenesh 44 , homology-based Fgenesh+ (http://www.softberry.com/) and ...


Molecular Plant Pathology
Volume 8 Issue 1 Page 111-120, January 2007

Isolation and characterization of the mating type locus of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana

LAURA CONDE-FERRAEZ et al.,
Centro de Investigacion Cientifica de Yucatan (CICY), Calle 43 no. 130, Chuburna de Hidalgo, C.P. 97200, Merida, Yucatan, Mexico

... Identification of open reading frames (ORFs) and gene predictions were performed using FGENESH and FGENESH+ software (Softberry™, http:/ / www.softberry.com ...


Insect Molecular Biology
15 (5), 541 - 549. doi:10.1111/j.1365-2583.2006.00674.x

Proteomic analyses of male contributions to honey bee sperm storage and mating

A. M. Collins, T. J. Caperna, V. Williams, W. M. Garrett, J. D. Evans
Bee Research Laboratory, ARS, USDA, Beltsville, MD, USA; *Growth Biology Laboratory, ARS, USDA, Beltsville, MD, USA; and Biotechnology and Germplasm Laboratory, ARS, USDA, Beltsville, MD, USA

... 2006) combined with a partially redundant database of ab initio proteins predicted by Genscan (Burge & Karlin, 1997) and FGENESH+ ( http:/ / www.softberry.com ...


J. Biol. Chem.,
Vol. 281, Issue 51, 39388-39395, December 22, 2006

A Toll Receptor and a Cytokine, Toll5A and Spz1C, Are Involved in Toll Antifungal Immune Signaling in the Mosquito Aedes aegypti*

Sang Woon Shin1, Guowu Bian1, and Alexander S. Raikhel2
From the Department of Entomology and the Institute for Integrative Genome Biology, University of California, Riverside, California 92521

... possible orthologues of Drosophila Toll and Toll-5. The open reading frames from these two loci were predicted using FGENESH+ (27) (sun1.softberry.com) by ...


Nature
434, 980-986 (21 April 2005)

The genome sequence of the rice blast fungus Magnaporthe grisea

Dean et al.,
Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina 27695, USA School of Biological and Chemical Sciences, University of Exeter, Washington Singer Laboratories, Exeter EX4 4QG, UK

...Gene predictions were performed using FGENESH/FGENESH1 + trained on M. grisea sequences (SoftBerry) and GENEWISE (Sanger Center) and validated against 65 characterized M. grisea genes. Additional information and gene identification...


Genome Research
14:685-692, 2004

Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human

Michael Brudno1 et al
1 Department of Computer Science, Stanford University, Stanford, California 94305, USA

... Fgenesh+ gene prediction is conducted on sequences with protein homology ...


Genome Research 13:313-322 2003
Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.313703.

A Complexity Reduction Algorithm for Analysis and Annotation of Large Genomic Sequences

Trees-Juen Chuang,1 et al
1Bioinformatics Research Center, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan;

...Numerous ab initio prediction programs have been used extensively in genome annotation, including FGENESH (Solovyev et al. 1995; Salamov and Solovyev 2000),
...Successful implementation of this method includes AAT (Huang et al. 1997), FGENESH+ and FGENESH++ (Salamov and Solovyev 2000),...
. Among these programs FGENESH+ (and FGENESH++), GenomeScan, GeneWise, and Procrustes are combined tools of sequence homology and ab initio annotation.


Annual Review of Genomics and Human Genetics Vol. 3: 293-310 (Volume publication date September 2002)

DATABASES AND TOOLS FOR BROWSING GENOMES

Ewan Birney,1 Michele Clamp,2 and Tim Hubbard2

1European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom; e-mail: birney@ebi.ac.uk
2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom; michele@sanger.ac.uk th@sanger.ac.uk

... Another predicted gene track on the UCSC browser comes from Softberry ( http:/ / www.softberry.com ) and uses a program Fgenesh+, which is based on HMMs and ...


FGENESH++

BMC Genomics
2016 17:540 DOI: 10.1186/s12864-016-2843-7

Evolutionary and functional analysis of mulberry type III polyketide synthases

Li, H. et al.,
State Key Laboratory of Silkworm Genome Biology, Southwest University

... All hits were analyzed using the Fgenesh++ program (http://www.softberry.com) [21, 48]. ...


Biotechnology and Bioengineering
2015 DOI 10.1002/bit.25864

Engineering Rhodosporidium toruloides for increased lipid production

Zhang et al.,
1: Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America. 2: Department of Bioengineering, University of California, Berkeley, California, United States of America.

... Genome annotation was performed using an automated software pipeline FGENESH++ (http://www.softberry.com) version 3.1.1. Genes were first predicted ab initio using FGENESH... Gene prediction parameters were obtained from Softberry and were based on Puccinia spp. ...


Nature Genetics
45, 456–461 (2013) doi:10.1038/ng.2569

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

Peng et al.,
Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China. National Center for Gene Research, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

... as used in genomic sequencing. Annotation of protein-coding genes. Protein-coding gene models were derived from evidence-based FgeneSH++(Softberry) pseudomolecules (Supplementary Fig. 7). To facilitate gene models ...


Nature Genetics
43, 913–918 (2011) doi:10.1038/ng.889

The genome of the extremophile crucifer Thellungiella parvula

Dassanayake et al.,
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. Office of Networked Information Technology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.

...Random shotgun genomic libraries were constructed according to the manufacturer's recommendations for each of the two pyrosequencing platforms, GS FLX Titanium (454 Life Sciences) and Illumina GA2 (Illumina). Newbler (454-Roche), ABySS29 and minimus2 (ref. 30) were used as the main assembly programs to generate the draft genome, and FGENESH++ (SoftBerry), GENSCAN, BLAST (see URLs) and Blast2GO12 were used to predict and annotate gene models. ... ...FGENESH++ (SoftBerry) was used to predict protein coding ORFs in the T. parvula draft genome masked for repetitive sequences, with parameters optimized for dicot plants and protein sequences from the NCBI non-redundant (NR) database as reference....


Insect Molecular Biology
Volume 19, Issue Supplement s2, pages 5–12, March 2010

AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome

Legeai et al.,
1 INRA UMR, Le Rheu cedex, France; 2 INRIA Centre Rennes – Bretagne Atlantique, GenOuest, Campus de Beaulieu, Rennes, France;

... Evidence-based prediction programs such as Augustus (Stanke et al., 2006), Fgenesh++ (unpubl., http://www.softberry.com) or the NCBI RefSeq pipeline are generally considered most reliable because they are better able to characterize untranslated regions (UTRs) and ... 


J. Proteome Res.
2010, 9 (2), pp 990–996 DOI: 10.1021/pr900885k

A Hybrid, de Novo Based, Genome-Wide Database Search Approach Applied to the Sea Urchin Neuropeptidome

Menschaert et al.,
Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Laboratory for Bioinformatics and Computational Genomics, Ghent University, B-9000 Ghent, Belgium

... The gene prediction program, Fgenesh++ (www.softberry.com), was applied to the genomic sequences corresponding to the newly identified peptides. The softberry gene finding software has a model trained for the sea urchin. ... 


Nature
2008, 452, 949 - 955.

The genome of the model beetle and pest Tribolium castaneum.

Richards et al.
1. Human Genome Sequencing Cente
2. Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

... Work at the BCM-HGSC was funded by grants from the NHGRI and USDA. FgenesH and FgenesH++ analysis was donated by Softberry Inc. This research was additionally supported in part by the Intramural...


Genome Biology
2006, 7(Suppl 1):S10 doi:10.1186/gb-2006-7-s1-s10

Automatic annotation of eukaryotic genes, pseudogenes and promoters

Victor Solovyev, Peter Kosarev, Igor Seledsov and Denis Vorobyev
Department of Computer Science, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
Softberry Inc., Radio Circle, Mount Kisco, NY10549, USA

... The Fgenesh++ gene prediction pipeline can identify 91% of coding nucleotides with a specificity of 90%. ...


Am. J. Hum. Genet.,
76:652-662, 2005

Position Effects Due to Chromosome Breakpoints that Map 900 Kb Upstream and 1.3 Mb Downstream of SOX9 in Two Patients with Campomelic Dysplasia

Gopalrao V. N. Velagaleti,1,2,* et al,.
Departments of 1Pathology and 2Pediatrics, University of Texas Medical Branch, Galveston; Departments of 3Molecular and Human Genetics and 4Pediatrics, Baylor College of Medicine, and 5Texas Children's Hospital, Houston; and 6Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN

...In an effort to identify possible transcripts that may be responsible for the CD phenotype, we used several gene-prediction programs and identified seven hypothetical transcripts in the region that spans 100 kb in either direction from the breakpoint on chromosome 17 Ecgenes H17C12306.1 and H17C12308.1, SGP genes Chr17_1538.1 and Ch17_1539.1, Fgenesh++ gene C17001650, and Genscan genes NT_010641.44 and NT_010641.45....


Genome Research
15:566-576, 2005

ECgene: Genome-based EST clustering and gene modeling for alternative splicing

Namshin Kim1,2, Seokmin Shin2 and Sanghyuk Lee1,3
1 Division of Molecular Life Sciences, Ewha Womans University, Seoul 120-750, Korea; 2 School of Chemistry, Seoul National University, Seoul 151-747, Korea

...the structure of full-length mRNA can be inferred by examining the flanking genomic region, especially with the aid of ab initio gene predicting programs such as Genscan (Burge and Karlin 1997 ) and Fgenesh++ (Salamov and Solovyev 2000 )...


Plant Physiology
139:1612-1624 (2005)

Structure and Architecture of the Maize Genome

Haberer et al.,
Munich Information Center for Protein Sequences, Institute for Bioinformatics, Gesellschaft fur Strahlenforschung Research Center for Environment and Health, D–85764 Neuherberg, Germany (G.H., H.G., K.F.X.M.); Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02141 (S.Y., C.R., S.R., B.B., C.N.);

... Genes were detected by applying FGeneSH++ (Salamov and Solovyev, 2000 Go ;


Genome Research
14:685-692, 2004

Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human

Michael Brudno1 et al.
1 Department of Computer Science, Stanford University, Stanford, California 94305, USA;

... we built a three-way synteny map based on chains of Fgenesh++-predicted (Solovyev 2002 ) exons, rather than whole genes. ...


Genome Research
14:539-548, 2004

Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes

Gregory M. Cooper1 et al
1 Department of Genetics, Stanford University, Stanford, California 94305, USA;

....The gene annotations used to classify the constrained elements contain nearly 40,000 genes, including RefSeq genes and gene predictions; they are based on annotations for the human, mouse, and rat genomes made by Fgenesh++ software developed by Softberry Inc. (Solovyev 2002; http://www.softberry.com )....


Nucleic Acids Research,
2003, Vol. 31, No. 1 207-211

The PEDANT genome database

Dmitrij Frishman*,1 et al
1 Institute for Bioinformatics, GSF - National Research Center for Environment and Health, Ingolstadter Landstra?e 1, 85764 Neueherberg, Germany

... The mouse database contains 20 chromosome contigs with 37 793 genes predicted using the Fgenesh++ software (www.softberry.com). ...


Genome Research
13:1765-1774, 2003

Identification of Promoter Regions in the Human Genome by Using a Retroviral Plasmid Library-Based Functional Reporter Gene Assay

Shirin Khambata-Ford1,5 et al
1 Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;

...Of 858 sequences, 9% of GFP+ low clones and 8% of GFP+ high clones aligned to the 2-kb segment upstream of the transcription start site of a predicted gene in at least two of four data sets of predicted genes from Genscan, Ensembl, Softberry (Fgenesh++), and Acembly (category B in Table 1).


Genome Research
13:313-322 ©2003
Received March 27, 2002; accepted in revised form December 3, 2002.
Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.313703.

A Complexity Reduction Algorithm for Analysis and Annotation of Large Genomic Sequences

Trees-Juen Chuang,1 et al
1Bioinformatics Research Center, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan;

...Numerous ab initio prediction programs have been used extensively in genome annotation, including FGENESH (Solovyev et al. 1995; Salamov and Solovyev 2000),
...Successful implementation of this method includes AAT (Huang et al. 1997), FGENESH+and FGENESH++ (Salamov and Solovyev 2000),...
. Among these programs FGENESH+ (and FGENESH++), GenomeScan, GeneWise, and Procrustes are combined tools of sequence homology and ab initio annotation.


Archives of Biochemistry and Biophysics
Volume 409, Issue 2, 15 January 2003, Pages 287-297

Mitochondrial and nucleocytoplasmic isoforms of O-linked GlcNAc transferase encoded by a single mammalian gene

Hanover et al.,
Laboratory of Cell Biochemistry and Biology, NIDDK, National Institutes of Health, Building 8, Room 402, 8 Center Drive, MSC 0850, NIH, Bethesda, MD 20892-0850, USA

... Ensembl, Fgenesh ++, and the TSSW Promoter Prediction algorithms (http://www.softberry.com/berry.phtml) were initially employed. ...


Cell,
Vol. 110, 521-529, August 23, 2002, Copyright .2002 by Cell Press

HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots

Astrid R.W. Schroder,1 et al
1Infectious Disease Laboratory

...An integration target sequence was scored as a part of a transcrip-tion unit if it was (1) a member of the Refseq set of well-studied genes (http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html) or (2) if , it was predicted to be a transcription unit by the ENSEMBLE (http://www.ensembl.org) or Fgenesh++ (http://www.softberry.com/Help/fgeneshplus2.htm) programs and if that assignment was supported by mRNA or spliced EST sequence evidence.


Genome Res.
2002. 12: 1549-1555

Mosaic Organization of Orthologous Sequences in Grass Genomes

Rentao Song, Victor Llaca 1, and Joachim Messing 2
Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854-8020, USA

... Gene prediction was based on both GeneScan (http://genes.mit.edu/Genscan.html) and FGENESH++ (http://www.softberry.com./berry.phtml?topic=gfind). ...


Reprint from
Daily Biotech Updates . . . www .genengnews.com

Vol. 22, No. 17 , October 1, 2002

DrugDiscovery
Tech Note:An Enhanced Human-Genome Database Transforming Raw Human Sequence Data Into Useful Information

Christine Schuller, Ph.D., and Andreas Fritz, Ph.D

The Softberry analysis results, for which Biomax has the exclusive world-wide commercial license, contain approximately 40,000 genes, which agrees well with predictions of the total number of human genes (according to the International Human Genome Sequencing Consortium, or IHGSC).
... For example, 50% of the genes in the Biomax Human Genome Database are not found in the Ensembl database. ..
These genes (identified by FGENESH++ and Biomax, and not found in Ensembl database) comprise the following: 6% of genes classified as known genes, 50% classified as having some similarity to known genes, and 90% of the genes not having similarity to known genes
For human genome applications, the FGENESH++ software was first used to map known human genes using sequences available from the Reference Sequence (RefSeq) Project at the Nation al Center for Biotechnology Information (NCBI; Bethesda, MD; www.ncbi.nlm. nih.gov/LocusLink/refseq.html).
REFERENCES
1. Salamov AA and Solovyev VV,Ab initio gene finding in Drosophila genomic DNA. Genome Res 10: 391-7 (2000).


FGENESH-C

The FASEB Journal
January 2013 vol. 27 no. 1 86-97 DOI:10.1096/fj.12-219444

Regulation of Anopheles gambiae male accessory gland genes influences postmating response in female

Dottorini et al.,
*Department of Experimental Medicine and †Department of Industrial Engineering, University of Perugia, Perugia, Italy; ‡Department of Biological Sciences, Imperial College London, South Kensington Campus, London, UK; and §Department of Genetics, University of Cambridge, Cambridge, UK

... The full-length sequence, structure, and the multiple variants of the HSF gene were predicted using FGENESH-C, FGENESH+ (http://linux1.softberry.com/), Wise2 (http://www.ebi.ac.uk/), and Genescan (http://genes.mit.edu/GENSCAN.html). Mosquito rearing and mating analysis. ...


Gene
Volume 528, Issue 2, 10 October 2013, Pages 267–276 DOI:10.1016/j.gene.2013.06.062

The metacaspase gene family of Vitis vinifera L.: Characterization and differential expression during ovule abortion in stenospermocarpic seedless grapes

Zhang et al.,
a College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China b Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling, Shaanxi 712100, China

... Intron and exon organizations of metacaspases were analyzed by using FGENESH-C (http://linux1.softberry.com/berryphtml?topic=fgenes_c&group=programs&subgroup=gfs); to determine the locations of metacaspases on chromosomes, the metacaspases were further used ...


The FASEB Journal
Published online before print September 20, 2012 DOI: 10.1096/fj.12-219444

Regulation of Anopheles gambiae male accessory gland genes influences postmating response in female

Dottorini et al.,
*Department of Experimental Medicine and †Department of Industrial Engineering, University of Perugia, Perugia, Italy; ‡Department of Biological Sciences, Imperial College London, South Kensington Campus, London, UK;

... The full-length sequence, structure, and the multiple variants of the HSF gene were predicted using FGENESH-C, FGENESH (http://linux1.softberry.com/), Wise2 (http:// www.ebi.ac.uk/), and Genescan (http://genes.mit.edu/ GENSCAN.html). Mosquito rearing and mating analysis ...


J. Exp. Bot.
(2011) 62 (15): 5641-5658. doi: 10.1093/jxb/err249

Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in the FRIGIDA homologue BnaA.FRI.a

Wang et al.,
1Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany 2Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China

... online). The genes were annotated using pairwise sequence alignments (BLAST2; http://www.ncbi.nlm.nih.gov) with FRI and the FGENESH+ and FGENESH_C gene prediction programs (http://linux1.softberry.com/berry.phtml). ...


J. Exp. Bot.
(2011) 62 (10): 3359-3374. doi: 10.1093/jxb/erq321

Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris

Abou-Elwafa et al.,
1Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany 2Broom's Barn Research Centre, Higham, Bury St. Edmunds, Suffolk IP28 6NP, UK

... Beta vulgaris sequences were annotated using pairwise sequence alignments (BLAST2; http://www.ncbi.nlm.nih.gov) against putative A. thaliana orthologues and the FGENESH+ and FGENESH_C gene prediction programs (http://linux1.softberry.com/berry.phtml) for ...


J. Exp. Bot.
2010 doi: 10.1093/jxb/erq321

Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris

Abou-Elwafa et al.,
1 Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany 2 Broom's Barn Research Centre, Higham, Bury St. Edmunds, Suffolk IP28 6NP, UK

.. Beta vulgaris sequences were annotated using pairwise sequence alignments (BLAST2; http://www.ncbi.nlm.nih.gov) against putative A. thaliana orthologues and the FGENESH+ and FGENESH_C gene prediction programs (http://linux1.softberry.com/berry.phtml) for ...


FGENESH-2

PLoS ONE
(2013), 8(1): e53525. doi:10.1371/journal.pone.0053525

A Genome-Wide Association Study Identifies Genomic Regions for Virulence in the Non-Model Organism Heterobasidion annosum s.s.

Dalman et al.,
Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden

...he gene annotations found in TC32-1 were transferred to the reference sequence using PROT_MAP, FGENESH-2 (SoftBerry, Mount Kisco, NY) and Artemis ...


Eukaryotic Cell
August 2010, p. 1225-1235, Vol. 9, No. 8 doi:10.1128/EC.00031-10

Methylenetetrahydrofolate Reductase Activity Is Involved in the Plasma Membrane Redox System Required for Pigment Biosynthesis in Filamentous Fungi

Frandsen et al.,
Division

... MTHFR homologs in complete Ascomycota genomes were identified in the listed databases using the blastp and tblastn algorithms with default settings (1). All Pezizomycotina tblastn hits were annotated using FGENEH-2 from Softberry (Mount Kisco, NJ) with FgMET13p as a ... 


J Immunol.
2010 Feb 1;184(3):1379-91. Epub 2009 Dec 21

A small, variable, and irregular killer cell Ig-like receptor locus accompanies the absence of MHC-C and MHC-G in gibbons

Abi-Rached et al.,
Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.

... Foster City, CA). Exons and introns of genes were either identified manually or by using the BLAST (www.ncbi.nlm.nih.gov/BLAST) and FGENESH-2 (www.softberry. com/all.htm) algorithms. Phylogenetic analysis of KIR. KIR gene ... 


The Journal of Immunology
2009, doi:10.4049/jimmunol.0903016

A Small, Variable, and Irregular Killer Cell Ig-Like Receptor Locus Accompanies the Absence of MHC-C and MHC-G in Gibbons

Abi-Rached et al.,
Department of Structural Biology, Stanford University, Stanford, CA 94305; Max Planck Institute for Molecular Genetics, Berlin-Dahlem

... Biosystems, Foster City, CA). Exons and introns of genes were either identified manually or by using the BLAST (www.ncbi.nlm.nih.gov/ BLAST) and FGENESH-2 (www.softberry.com/all.htm) algorithms. Phylogenetic analysis of KIR ...


PLoS Genet.
2009 Oct;5(10):e1000688. Epub 2009 Oct 16.

A novel system of polymorphic and diverse NK cell receptors in primates

Averdam et al.,
Department of Primate Genetics, German Primate Centre, Gottingen, Germany.

... Both programs are available from Phil Green, University of Washington. Exons and introns of genes were identified in finished BAC clone sequences manually or by BLAST and FGENESH-2 algorithms (http://www.ncbi.nlm.nih.gov/BLAST/; http://www.softberry.com/all.htm). ...


The Journal of Immunology
2007, 178: 7151-7161.

Genomics and Diversity of the Common Marmoset Monkey NK Complex

Anne Averdam et al.,
Department of Primate Genetics and Primate Husbandry, German Primate Center, Gottingen, Germany; Max Planck Institute for Molecular Genetics, Berlin, Germany; and Department of Biological Sciences, University of South Carolina, Columbia, SC 29208

... BLAST and FGENESH-2 algorithms (http://www.ncbi.nlm.nih.gov/BLAST/; http://www.softberry.com/all.htm) identified exons and introns of genes in finished BAC ...


FGENESH++C

Nucleic Acids Research,
2006, Vol. 34, Database issue D568-D571

The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context

Andreas Ruepp1,* et al.,
1Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany

... The basis of the MfunGD dataset is a complement of gene products that was obtained by Softberry Inc., which used the FGENESH++C software as gene predictor. ...


Nature
425, 209-215 (11 September 2003) | doi:10.1038/425209a

Bioinformatics: Programmed for success

Steve Buckingham

... Three-way synteny from Softberry. Fast searching is also a feature of Genome Explorer from Softberry in Mount Kisco, New York, which uses the FMAP algorithm. ... ...... Softberry, for example, offers a number of gene-prediction programs that can be accessed over the web, including FGENESH, which ... The fully automated FGENESH++C will automatically annotate any genome (other than human) to a standard claimed to be indistinguishable ...



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