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The programs usage in Scientific publications
FGENESV, FGENESV0
Archives of Virology
2016, 1-4. doi:10.1007/s00705-016-3005-6
The complete genome sequence of PE3-1, a novel E. coli O153 phage
Liu, H. et al.,
College of Resources and Environmen tUniversity of Chinese Academy of Sciences
... Potential ORFs were predicted using ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html),
and ORFs were further identified using GLIMMER (ver.3.02) [15] and the ''Gene Finding in Viral
Genomes'' function in Softberry (http://linux1.softberry.com/all.htm). ...
Genome Announcements
2016, 4(3), e00536-16. doi: 10.1128/genomeA.00536-16
Genome sequence of Vaccinia virus strain Lister-Butantan, a Lister vaccine variant used during a smallpox eradication campaign in Brazil
Assis, F. et al.,
aLaboratorio de Virus do Instituto de Ciencias Biologicas da Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
bNational Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention, Atlanta, Georgia, USA
... Chromatogram data were assembled using SeqMerge (Accelrys, Inc., Madison, WI), Phred/Phrap
was used for base-calling and assembly software, and Consed was used for sequence editing.
The FgenesV tool was used for gene prediction (http://www.softberry.com/). ...
Genome Announcements
2016, 4(3), e00601-16. doi: 10.1128/genomeA.00601-16
Complete genome sequences of T1-like phages JMPW1 and JMPW2
Shen, M. et al.,
Department of Microbiology, College of Basic Medical Science, Third Military Medical University, Chongqing, People’s Republic of China
... Genome annotations of the phages were revealed using fgenesV (http://linux1.softberry.com/
berry.phtml?topic=virus&group=programs&subgroup=gfindv) and manually verified by screening
all the predicted proteins against the NCBI protein database using BLASTp (6). Then ...
Evolutionary Bioinformatics Online
2016, 12(Suppl 2), 1. doi: 10.4137/EBO.S38518
Bioinformatic Characterization of Mosquito Viromes within the Eastern United States and Puerto Rico: Discovery of Novel Viruses
Frey, K. G. et al.,
1Naval Medical Research Center – Frederick, Fort Detrick, MD, USA.
2Henry M. Jackson Foundation, Bethesda, MD, USA.
3Hood College, Frederick, MD, USA
... A second in silico gene finder, FGENESV (linux1.softberry.com), confirmed the four ORFs. ...
Viruses
2016, 8(3), 76; doi:10.3390/v8030076
A Brazilian Marseillevirus Is the Founding Member of a Lineage in Family Marseilleviridae
Dornas, F. P. et al.,
1 Laboratorio de Virus, Departamento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
2 Unite de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculte de Medecine, Marseille 13385, France
... Gene predictions were performed using FgenesV [31], RAST (Rapid Annotation using Subsystem Technology) [32] and GeneMarkS [33] tools, and merged. ...
Journal of Invertebrate Pathology
2016, 139, 56-66. doi:10.1016/j.jip.2016.07.011
An alphabaculovirus isolated from dead Lymantria dispar larvae shows high genetic similarity to baculovirus previously isolated from Lymantria monacha–An example of adaptation to a new host
Rabalski, L., Krejmer-Rabalska, M., Skrzecz, I., Wasag, B., Szewczyk, B.
a Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Laboratory of Recombinant Vaccines, Abrahama Str. 58, 80-307 Gdansk, Poland
b Forest Research Institute, Department of Forest Protection, Raszyn Braci Lesnej Str. 3, 05-090 Sekocin Stary, Poland
... ORFs were identified using Glimmer3 (gene model pre-computed on RefSeq LdMNPV genome (NC_001973)) (Delcher et al., 2007),
GeneMarkS (parameter: intron less eukaryotic-virus) (Borodovsky and McIninch, 1993)
(http://linux1.softberry.com/berry.phtml?topic=virus0&group=programs&subgroup=gfindv), and tcode EMBOSS 6.5.7 (Rice et al., 2000)....
PloS one
2016, 11(7), e0160389. doi: 10.1371/journal.pone.0160389
The Complete Genome Sequence of Plodia Interpunctella Granulovirus: Evidence for Horizontal Gene Transfer and Discovery of an Unusual Inhibitor-of-Apoptosis Gene
Harrison, R. L., Rowley, D. L., Funk, C. J.
Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, Maryland, United States of America
Department of Biology, John Brown University, Siloam Springs, Arkansas, United States of America
.. eg no matches with
e-values <0.010) were annotated if they did not overlap a larger ORF by >75 bp and if they were
predicted to be protein-encoding by both the fgenesV (http://linux1.softberry.com/berry ...
BULLETIN OF THE EUROPEAN ASSOCIATION OF FISH PATHOLOGISTS
2016, 36(1), 11-23.
Novel viral infections threatening Cyprinid fish
Haenen, O. et al.,
1 Central Veterinary Institute of Wageningen UR, The Netherlands; 2 Centre for Environment, Fisheries
and Aquaculture Science (CEFAS), Weymouth DT4 8UB, England
... Fish Pathol., 36(1) 2016, 19 sembler), (Hunt et al., 2015). Surprisingly a 16 kb putative viral
sequence was generated and subsequently annotated using a selection of bioinformatics tools
including FGENESV0 (htp://linux1.softberry.com), Prokka (Seemann, 2014) and BLAST. ...
PloS one
2016, 11(5), e0155134 doi: 10.1371/journal.pone.0155134
Genome Sequencing and Analysis of Catopsilia pomona nucleopolyhedrovirus: A Distinct Species in Group I Alphabaculovirus
Wang, J. et al.,
State Key Laboratory of Virology and China Center for Virus Culture Collection, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
...Putative ORFs were analyzed
using the FGENESV0 program (http://www.softberry.com/berry.phtml) [48] and the
NCBI ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). ...
J. Gen. Virol.
March 2016 97: 706-714, doi: 10.1099/jgv.0.000394
A Cripavirus in the brown planthopper, Nilaparvata lugens
Wang, S. L., Cheng, R. L., Lu, J. B., Yu, X. P., Zhang, C. X.
1? State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Science, Zhejiang University, Hangzhou, Zhejiang 310058, PR China 2? College of Life Science, China Jiliang University, Hangzhou, Zhejiang 310018, PR China
... The NlCV genome sequence comprised 9144 nt, excluding the 3! poly(A) tail, with 37.8 %
GC content. The coding sequence (CDS) of the virus genome was predicted through
the FGENESV0 program in SoftBerry (http://linux1.softberry. ...
Genome Announcements
2016, 4(3), e00115-16. doi: 10.1128/genomeA.00115-16
Complete genome sequence of bacteriophage Deep-Blue infecting emetic Bacillus cereus
Hock, L., Gillis, A., Mahillon, J.
Laboratory of Food and Environmental Microbiology, Universite Catholique de Louvain, Louvain-la-Neuve, Belgium
... Genome Announc 4(3):e00115-16. doi:10.1128/genomeA.00115-16. Copyright © 2016 Hock
et al. ... The potential coding sequences (CDSs) were pre- dicted using Glimmer v3.02 (5), RAST
2.0 (6), GenMarkS 2.5p (7), and FgenesV (http://www.softberry.com/). ...
Veterinary microbiology
2016, 182, 135-140. doi:10.1016/j.vetmic.2015.11.015
Genomic characterisation of canine papillomavirus type 17, a possible rare cause of canine oral squamous cell carcinoma
Munday, J. S., Dunowska, M., Laurie, R. E., Hills, S.
a College of Science, Massey University, Palmerston North, New Zealand
b Otago Genomics and Bioinformatics Facility, Otago University, Dunedin, New Zealand
... 8.04 software (Drummond et al., 2010). 2.3. DNA and protein sequence analysis.
The putative coding regions in the PV sequence were predicted using FGENESV0
(http://linux1.softberry.com). The characteristics of the putative ...
Virus genes
2016, 1-7. DOI: 10.1007/s11262-016-1340-z
Genomic characterization of a novel Epsilonpapillomavirus associated with pigmented papillomas in a red deer (Cervus elaphus)
Munday, J. S. et al.,
1. College of Science, Massey University, Palmerston North, New Zealand
2. Gribbles Veterinary Pathology, Palmerston North, New Zealand
... Geneious version 8.04 software [12]. DNA and protein sequence analysis The
putative coding regions in the PV sequence were predicted using FGENESV0
(http://linux1.softberry.com). The characteristics of the putative viral ...
Archives of virology
2016, 161(1), 209-212. DOI: 10.1007/s00705-015-2608-7
Genome sequence of a cluster A13 mycobacteriophage detected in Mycobacterium phlei over a half century ago
Marton, S. et al.,
1. Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungaria krt 21, 1143, Budapest, Hungary
2. Biological Research Centre, Hungarian Academy of Sciences, Temesvari krt. 62, 6726, Szeged, Hungary
... with MIRA 4.0. GeneMarkS, FGENESV [http://www.softberry.com/], Glimmer 3.02
and DNA Master 5.22.9 software were applied for genome annotation and gene
prediction [1–3, 15; http:// phagesdb.org/]. Protein homology was ...
Virologica Sinica
2015, 30(6), 417-424. DOI: 10.1007/s12250-015-3658-4
Genome sequencing and analysis of a granulovirus isolated from the Asiatic rice leafroller, Cnaphalocrocis medinalis
Zhang et al.,
1. State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China
2. State Key Laboratory of Virology and China Center for Virus Culture Collection, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
... nih.gov/genbank). Hypothetical ORFs were predicted by soft berry FGENESV program
(http://www.softberry.com/berry. phtml) (Solovyev and Salamov, 1999) and defined by the standard
ATG start, and a stop codon and potentially en- code at least 50 amino acids. ...
Genome announcements
2015, 3(6), e01192-15. doi: 10.1128/genomeA.01192-15
First complete genome sequence of Felis catus gammaherpesvirus 1
Troyer, R. M. et al.,
aDepartment of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA
bDepartment of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
... We verified the final sequence by reassembly of the MiSeq reads to the consensus genome using
Bowtie2 (8). We defined open reading frames (ORFs) by prediction with GeneMarkS (9) and
FGENESV (SoftBerry) and comparison to herpesvirus and cellular genes using NCBI ...
PloS one
2014, 9(1), e86450. DOI:10.1371/journal.pone.0086450
Genome Sequence and Analysis of Buzura suppressaria Nucleopolyhedrovirus: A Group II Alphabaculovirus
Zhu Z. et al.,
State State Key Laboratory of Virology and China Center for Virus Culture Collection, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
Canadian Forest Service, Great Lakes Forestry Centre, Sault Ste Marie, Ontario, Canada
... KF611977). Hypothetical ORFs were predicted by softberry FGENESV program
(http://www.softberry.com/berry.phtml) [58] to contain the standard ATG start, and a
stop codon and potentially encode at least 50 amino acids. Gene ...
Virus research
2014, 185, 110-113 DOI:10.1016/j.virusres.2014.02.019
The genomic RNA1 and RNA2 sequences of the tobacco rattle virus isolates found in Polish potato fields
Yin Z. et al.,
a Mlochow Research Center, Plant Breeding and Acclimatization Institute – National Research Institute, Platanowa Street 19, PL-05-831 Mlochow, Poland
b Department of Plant Genetics, Breeding & Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences – SGGW, Nowoursynowska Street 159, PL-02-776 Warsaw, Poland
... SeqMan Pro. Version 9.1.0 (109) 418. Gene structure annotation was predicted by
two software packages, GenMark (Besemer and Borodovsky, 1999, http://exon.gatech.
edu/) and fgenesV0 (http://linuxl.softberry.com). The models ...
Archives of virology
2014, 1-5. DOI:10.1007/s00705-014-2128-x
Single-nucleotide polymorphisms and reading frame shifts in RNA2 recombinant regions of tobacco rattle virus isolates Slu24 and Deb57
Yin, Z., Pawelkowicz, M., Michalak, K., Chrzanowska, M., & Zimnoch-Guzowska, E.
1. Mlochow Research Center, Plant Breeding and Acclimatization Institute - National Research Institute, Platanowa Street 19, 05-831, Mlochow, Poland
2. Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences-SGGW, Nowoursynowska Street 159, 02-776, Warsaw, Poland
... The corresponding bands were purified using a QIAquick Gel Extraction Kit (QIAGEN) and
sequenced directly. Gene structure annotation was done using two software packages, GenMark
[4, http:// exon.gatech.edu/] and fgenesV0 [http://linuxl.softberry. com]. ...
Applied and environmental microbiology
2014, 80(1), 374-384. DOI:10.1128/AEM.02279-13
Genomic Investigation of Lysogen Formation and Host Lysis Systems of the Salmonella Temperate Bacteriophage SPN9CC
Shin, H., Lee, J. H., Yoon, H., Kang, D. H., Ryu, S.
a Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
b Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
... The prediction of open reading frames (ORFs) was conducted with Glimmer 3.02 (33), GeneMarkS
(34), and FgenesV (Softberry, Inc., Mount Kisco, NY). The prediction of ribosomal binding sites
of ORFs was performed with RBSfinder (J. Craig Venter Institute, Rockville, MD). ...
Virus genes
2014, , 48(1), 111-119. DOI: 10.1007/s11262-013-1002-3
Genomic characterisation of Felis catus papillomavirus 4, a novel papillomavirus detected in the oral cavity of a domestic cat
Dunowska, M., Munday, J. S., Laurie, R. E., Hills, S. F.
1. Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Tennent Drive, Palmerston North, 4474, New Zealand
2. Biochemistry Department, Otago University, Dunedin, New Zealand
... Sequence analysis The putative coding regions in the PV sequence were predicted
using FGENESV0 (http://linux1.softberry.com). The characteristics of the putative
viral proteins, the pre- sence of conserved protein domains ...
Virus Genes
November 2013 DOI:10.1007/s11262-013-1002-3
Genomic characterisation of Felis catus papillomavirus 4, a novel papillomavirus detected in the oral cavity of a domestic cat
Magdalena Dunowska, John S. Munday, Rebecca E. Laurie, Simon F. K. Hills
1. Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Tennent Drive, Palmerston North, 4474, New Zealand
2. Biochemistry Department, Otago University, Dunedin, New Zealand
... Sequence analysis The putative coding regions in the PV sequence were predicted
using FGENESV0 (http://linux1.softberry.com). The characteristics of the putative
viral proteins, the pre- sence of conserved protein domains ...
Virus Genes.
2013 Aug;47(1):133-51. doi: 10.1007/s11262-013-0922-2. Epub 2013 May 28.
Complete genomic sequences and comparative analysis of Mamestra brassicae nucleopolyhedrovirus isolated in Korea
Choi et al.,
Department of Agricultural Biology, College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju, Republic of Korea.
... Sequence data were assembled and analysed using Lasergene7 software (DNASTAR). Putative
open reading frames (ORFs) were analysed using the FGENESV0 (http://linux1.softberry.com/
berry.phtml) and the NCBI ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). ...
Veterinary Microbiology
Volume 165, Issues 3–4, 30 August 2013, Pages 319–325 DOI:10.1016/j.vetmic.2013.04.006
Genomic characterization of Felis catus papillomavirus-3: A novel papillomavirus detected in a feline Bowenoid in situ carcinoma
John S. Munday a, Magda Dunowska a, Simon F. Hills a, Rebecca E. Laurie b
a College of Sciences, Massey University, Palmerston North, New Zealand
b Biochemistry Department, Otago University, 710 Cumberland Street, Dunedin, New Zealand
... primer sequences available on request). 138 2.3 DNA and protein sequence analysis
The putative coding regions in the PV sequence were predicted using FGENESV0
141 (http://linux1.softberry.com). The characteristics of the ...
Appl. Environ. Microbiol.
March 2013 vol. 79 no. 6 1956-1968 doi: 10.1128/?AEM.02793-12
wksl3, a New Biocontrol Agent for Salmonella enterica Serovars Enteritidis and Typhimurium in Foods: Characterization, Application, Sequence Analysis, and Oral Acute Toxicity Study
Hyun-Wol Kang a, Jae-Won Kim b, Tae-Sung Jung c and Gun-Jo Woo a
aFood Safety and Evaluation Laboratory, Department of Food Bioscience and Technology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, Republic of Korea
bCJ Research Institute of Biotechnology, CJ CheilJedang, Seoul, Republic of Korea
... with SeqMan II sequence analysis software (DNASTAR). Possible open reading frames (ORFs)
were predicted with the genome annotation software GeneMarkS (28) and confirmed with FgenesV
(SoftBerry) and Glimmer 3.02 (29) by submitting the whole genome of wksl3. ...
PLoS ONE
7(5): e37557. doi:10.1371/journal.pone.0037557
Genome Characteristics of a Novel Phage from Bacillus thuringiensis Showing High Similarity with Phage from Bacillus cereus
Yihui Yuan,
Meiying Gao,
Dandan Wu,
Pengming Liu,
Yan Wu
Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
... Each base had at least five-fold coverage. Open reading frames (ORFs) were predicted
with FGENESV software (http://linux1.softberry.com/berry.phtml??topic=virus&group=
programs&subgroup=gfin?dv) and by visual inspection. ...
J. Virol.
August 2012 vol. 86 no. 15 8014-8030 DOI: 10.1128/JVI.00723-12
A Novel Bat Herpesvirus Encodes Homologues of Major Histocompatibility Complex Classes I and II, C-Type Lectin, and a Unique Family of Immune-Related Genes
Huajun Zhang et al.,
aCSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia
bWuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
... Computer-assisted analysis.Open reading frames (ORFs) were initially predicted with the software
programs FgenesV (Softberry) and GeneMarkS (5). ORFs that contained canonical start and
stop codons were BLASTed against the local protein database of betaherpesviruses ...
PLoS One;
2011 May Journal Volume: 5; Journal Issue: 1;
Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community
Reddy et al.,
... the BLAST scores. After manual frameshift correction, genes were called using fgenesb
(http:// www.softberry.com). For phylogenetic ... to Iodobacteriophage. Genes were
predicted using fgenesV (www. softberry.com). Found at: doi ...
J. Virol.
May 2012 vol. 86 no. 9 5039-5054 DOI: 10.1128/JVI.07162-11
Biological Characterization and Next-Generation Genome Sequencing of the Unclassified Cotia Virus SPAn232 (Poxviridae)
Afonso et al.,
aLaboratorio de Biologia Molecular de Virus
bLaboratorio de Ultraestrutura Hertha Meyer, Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
... with default parameters. Open reading frames (ORFs) longer than 30 amino acids
were detected by FGENESV (Softberry), Vector NTI (Invitrogen), and CLC DNA
Workbench (CLC bio, Aarhus, Denmark). Predicted ORFs containing ...
Aquat Biol
Vol. 14: 223–232, 2012
doi: 10.3354/ab00395
Genetic diversity of the Caribbean spiny lobster
virus, Panulirus argus virus 1 (PaV1), and the
discovery of PaV1 in lobster postlarvae
Jessica Moss
1,
*, Mark J. Butler IV 2, Donald C. Behringer 3, Jeffrey D. Shields 1
1
Department of Environmental and Aquatic Animal Health, Virginia Institute of Marine Science, Greate Road,
Gloucester Point, Virginia 23062, USA
2
Department of Biological Sciences, Old Dominion University, Norfolk, Virginia 23529, USA
... FgenesV (http:// linux1. softberry. com/), a trained pattern/Markov chain-based viral gene
prediction program, was used to translate the sequenced region and to identify ORFs or
possible viral genes. RESULTS PaV1 detection by PCR Postlarvae ...
PLoS ONE
7(8): e43106. doi:10.1371/journal.pone.0043106
Isolation and Characterization of Three Mammalian Orthoreoviruses from European Bats
Kohl et al.,
Robert Koch Institute, Centre for Biological Security 1, Berlin, Germany
... Pro package. The sequence was also analyzed by the FGENESV Trained
Pattern/Markov chain-based viral gene prediction program (http://www.softberry.com).
Phylogenetic Tree Reconstruction. Multiple alignments (ClustalW ...
Appl. Environ. Microbiol.
January 2012 vol. 78 no. 1 58-69 DOI: 10.1128/AEM.06231-11
Characterization and Comparative Genomic Analysis of a Novel Bacteriophage, SFP10, Simultaneously Inhibiting both Salmonella enterica and Escherichia coli O157:H7
Park et al.,
aDepartment of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, and Center for Agricultural Biomaterials, Seoul National University, Seoul, South Korea
bLaboratory of Food Microbiology and Functional Genomics, Department of Food Science and Biotechnology, CHA University, Seongnam, South Korea
... Prediction of all open reading frames (ORFs) was carried out using the Glimmer by
GAMOLA automatic annotation program (1) and confirmed using GeneMark (5) and
FgenesV software (Softberry, Inc., Mount Kisco, NY). Annotation ...
BMC Microbiology
2012, 12:297
http://www.biomedcentral.com/1471-2180/12/297
Characteristics of a broad lytic spectrum
endolysin from phage BtCS33 of Bacillus thuringiensis
Yihui Yuan, Qin Peng and Meiying Gao *
Key Laboratory of Agricultural and Environmental Microbiology, Wuhan
Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R.
China
...Open reading frames (ORFs) of the phage BtCS33 genome
(GenBank: JN191664) were predicted using FGENESV
software (http://linux1.softberry.com/berry.phtml?topic=-
virus&group=programs&subgroup=gfindv) and by visual
inspection. ...
Environmental Microbiology
Special Issue: Microbial Communities - Structure, Behaviour, Evolution
Volume 14, Issue 9, pages 2564–2576, September 2012 DOI: 10.1111/j.1462-2920.2012.02775.x
Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses
David T. Pride 1,*, Julia Salzman 2, David A. Relman 3,4,5
1 Departments of Pathology and Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA 92093-0612, USA
2Departments of Biochemistry and Statistics
3 Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
... spacers. Viral contigs were analysed using FGenesV (Softberry, Mount Kisco, NY)
for open reading frame prediction, and individual open reading frames analysed using
blastX analysis against the NCBI non-redundant database. ...
Research in Microbiology
Volume 163, Issue 3, April 2012, Pages 233–241 http://dx.doi.org/10.1016/j.resmic.2012.01.002,
Characterization of endolysin from a Salmonella Typhimurium-infecting bacteriophage SPN1S
Jeong-A. Lim ,
Hakdong Shin ,
Dong-Hyun Kang ,
Sangryeol Ryu
Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
... 2. Materials and methods. 2.1. Bioinformatic analysis. Prediction of ORFs in the lysis cluster of
the SPN1S genome was done using Glimmer 3.02 (Delcher et al., 2007), GeneMark.hmm
(Lukashin and Borodovsky, 1998) and FgenesV software (http://www.softberry.com). ...
Archives of Virology
August 2012, Volume 157, Issue 8 , pp 1559-1564 DOI
10.1007/s00705-012-1316-9
Sequencing and analysis of the complete genome of Rana grylio virus (RGV)
Xiao-Ying Lei (1)
Tong Ou (1)
Ruo-Lin Zhu (1)
Qi-Ya Zhang zhangqy@ihb.ac.cn (1)
1. State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Wuhan, 430072, China
... Madison, WI, USA). The ORFs were predicted using Gene Finding in the virus genome
program at the website http://www.softberry.com and NCBI ORF Finder (http://www.
ncbi.nlm.nih.gov/gorf/ gorf.html). Comparisons of homologous ...
J. Virol.
doi: 10.1128/?JVI.01796-12 October 2012 vol. 86 no. 19 10894
Complete Genome Sequence of Bacteriophage SSU5 Specific for Salmonella enterica serovar Typhimurium Rough Strains
Minsik Kim,
Sujin Kim and
Sangryeol Ryu
Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, and Center for Agricultural Biomaterials, Seoul National University, Seoul, South Korea
... GS De Novo assembler (v. 2.60) was used to assemble quality filtered reads, and GeneMarkS
(2), Glimmer 3.02 (4), and FgenesV (Softberry, Inc., Mount Kisco, NY) were used to predict open
reading frames (ORFs) that encode proteins of more than 40 amino acids. ...
J. Virol.
doi: 10.1128/?JVI.01579-12 September 2012 vol. 86 no. 18 10234-10235
Complete Genome Sequence of Caulobacter crescentus Bacteriophage phiCbK
Gael Panis a,
Christophe Lambert b and
Patrick H. Viollier a
aDepartment of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
bProgenus S.A., Gembloux, Belgium
.. of ?CbK genomic DNA (extracted using the Norgen Biotek phage DNA extraction kit), we
assembled quality-filtered reads (Velvet 01.01.04 software), predicted coding sequences (pCDS),
and transfer RNAs (tRNAs) using Glimmer3.02 (4), FgenesV (Softberry, Inc., Mount Kisco ...
J. Virol.
doi: 10.1128/?JVI.01529-12 September 2012 vol. 86 no. 17 9552
Genome Sequence of a Novel Actinophage PIS136 Isolated from a Strain of Saccharomonospora sp.
Richa Bajpai et al.,
aInstitute of Microbial Technology, CSIR, Chandigarh, India
bInstitute of Genomics and Integrative Biology, CSIR, Delhi, India
... The open reading frames (ORFs) were predicted using FGENESV (SoftBerry, Inc., Mount Kisco,
NY) and GeneMark (1). After manual curation, a total of 132 ORFs (61 ORFs on the positive strand
and 71 on the negative strand) were annotated by using homology search at the ...
J. Virol.
doi: 10.1128/?JVI.00636-12 June 2012 vol. 86 no. 11 6367-6368
Complete Genome Sequence of Cronobacter sakazakii Bacteriophage CR3
Hakdong Shin a,
Ju-Hoon Lee b,
Yeran Kim a and
Sangryeol Ryu a
aDepartment of Food and Animal Biotechnology, Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul, South Korea
bDepartment of Food Science and Biotechnology, Kyung Hee University, Yongin, South Korea
... Korea. The quality-filtered reads were assembled using Newbler 2.3, and the prediction
of open reading frames (ORFs) was performed using GeneMarkS (1), Glimmer3 (2),
and FgenesV (Softberry, Inc., Mount Kisco, NY). Transfer ...
Nucl. Acids Res.
(2012) 40 (W1): W186-W192. doi: 10.1093/nar/gks528
VIGOR extended to annotate genomes for additional 12 different viruses
Shiliang Wang 1,*,
Jaideep P. Sundaram 2 and
Timothy B. Stockwell 1
1J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850 and 2Genomics Department, BioReliance Corporation, 14920 Broschart Rd, Rockville, MD 20850, USA
... These complex gene features must be accurately defined in order to correctly
understand these genomes. Universal gene prediction programs, such as FgenesV
(www.softberry.com) and Zcurve_V (1), are available for public use. ...
J. Virol.
doi: 10.1128/?JVI.07226-11 March 2012 vol. 86 no. 6 3404-3405
Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Bacteriophage SPN3UB
Ju-Hoon Lee b,
Hakdong Shin a and
Sangryeol Ryu a
aDepartment of Food and Animal Biotechnology and Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul, South Korea
bDepartment of Food Science and Biotechnology, CHA University, Seongnam, South Korea
... Assembly of quality filtered reads was performed using a 454 Newbler 2.3 assembler,
and open reading frames (ORFs) were predicted using GeneMarkS (5), Glimmer
3.02 (9), and FgenesV (Softberry, Inc., Mount Kisco, NY). ...
J. Virol.
doi: 10.1128/?JVI.06696-11 January 2012 vol. 86 no. 2 1284-1285
Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Bacteriophage SPN1S
Hakdong Shin a,
Ju-Hoon Lee b,
Jeong-A Lim a,
Hyeryen Kim a and
Sangryeol Ryu a
aDepartment of Food and Animal Biotechnology, Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul, Korea
bDepartment of Food Science and Biotechnology, CHA University, Seongnam, Korea
... From the complete genome sequence of phage SPN1S, open reading frames (ORFs)
were predicted using the GAMOLA automatic annotation program (1) and confirmed
using GeneMarkS (3), Glimmer 3.02 (6), and FgenesV (SoftBerry). ...
J. Virol.
January 2012 vol. 86 no. 1 637-638 doi: 10.1128/?JVI.06520-11
Complete Genome Sequence of Bacillus cereus Bacteriophage BCP78
Ju-Hoon Lee b,
Hakdong Shin a,
Bokyung Son a and
Sangryeol Ryu a
aDepartment of Food and Animal Biotechnology, Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, South Korea
bDepartment of Food Science and Biotechnology, CHA University, Seongnam 463-836, South Korea
... The assembly of quality filtered reads was performed using 454 Newbler 2.3 assembler, and
the prediction of open reading frames (ORFs) and their confirmation were conducted using the
Glimmer 3.02 (3), GeneMark.hmm (10), and FgenesV softwares (Softberry, Inc., Mount ...
Extremophiles
September 2012, Volume 16, Issue 5, pp 715-726 DOI
10.1007/s00792-012-0467-7
Genome sequence of temperate bacteriophage Psymv2 from Antarctic Dry Valley soil isolate Psychrobacter sp. MV2
Tracy L. Meiring (1)
I. Marla Tuffin (1)
Craig Cary (2)
Don A. Cowan (1)
1. Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Office 2117, Level 2 Life Sciences Building, Modderdam Rd, Bellville, 7535, South Africa
2. Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
... Ab initio gene predictions were performed using GeneMark.hmm 2.0 (http://www.exon.biology.
gatech.edu/heuristic_hmm2.cgi) (Besemer and Borodovsky 1999), fgenesv and fgenesb
(http://www.linux1.softberry.com/berry.phtml) (Softberry, Mount Kisco, NY, USA) using the ...
Australasian Plant Disease Notes
April 2012 DOI
10.1007/s13314-012-0048-8
Clitoria yellow mottle virus: a tobamovirus from Northern Australia
Kejun Wei (1)
Adrian Gibbs (2)
Anne Mackenzie (3)
1. Faculty of Applied Science, University of Canberra, Canberra, ACT, 2617, Australia
2. Australian National University Emeritus Faculty, Canberra, ACT, 0200, Australia
3. CSIRO Division of Plant Industry, Canberra, ACT, 2601, Australia
... The genome of CYMV has the same structure as most other tobamoviruses (Stobbe
et al. 2011). The MolQuest- Softberry viral gene detector (http://www.softberry.com)
found four open reading frames (ORFs) in the CYMV sequence. ...
J. Virol.
March 2011 vol. 85 no. 6 2642-2656 DOI: 10.1128/JVI.01661-10
Identification and Sequencing of a Novel Rodent Gammaherpesvirus That Establishes Acute and Latent Infection in Laboratory Mice
Loh et al.,
1Department of Pathology and Immunology
2Department of Molecular Microbiology
3Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
... Viral genome and phylogenetic analyses.Predicted ORFs were identified using Geneious (see
above), fgenesV (SoftBerry, Mount Kisco, NY) (13, 69), and GeneMark (6) and were analyzed
using BLAST algorithms (3). ORFs that were predicted by both fgenesV and GeneMark ...
J. Virol.
October 2011 vol. 85 no. 19 10230-10238 DOI: 10.1128/JVI.00637-11
The Genome of Yoka Poxvirus
Zhao et al.,
1 Departments of Pathology and Immunology and Molecular Microbiology, Washington University School of Medicine, and the Midwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, St. Louis, Missouri
2 Department of Pathology, University of Texas Medical Branch, Galveston, Texas
... described for other recently sequenced poxviruses (1, 2, 23). Briefly, ORFs were
predicted using FgenesV (SoftBerry, Inc.; www.softberry.com/) and Getorf (Emboss
package). All predicted ORFs of more than 90 nucleotides with ...
J. Virol.
December 2011 vol. 85 no. 24 13470-13471 doi: 10.1128/JVI.06344-11
Complete Genome Sequence of Salmonella Bacteriophage SPN3US
Ju-Hoon Lee 1, Hakdong Shin 2, Hyeryen Kim 2 and Sangryeol Ryu 2
1Department of Food Science and Biotechnology, CHA University, Seongnam 463-836, South Korea
2Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, South Korea
... Prediction of open reading frames (ORFs) was performed using the GAMOLA automatic
annotation program (1), and predicted ORFs were confirmed using the Glimmer 3.02 (5),
GeneMark.hmm (7), and FgenesV (Softberry, Inc., Mount Kisco, NY) software. ...
Virus Research
Volume 160, Issues 1–2, September 2011, Pages 128–135 DOI: 10.1016/j.virusres.2011.05.023
Genomic and phylogenetic analyses of murine adenovirus 2
Hemmi et al.,
a Institute of Molecular Life Sciences, University of Zurich, Switzerland
b Veterinary Medical Research Institute, Hungarian Academy of Sciences, Budapest, Hungary
... annular.org/sdbrown/dna/translator.html). The sequence was also analyzed by the
FGENESV Trained Pattern/Markov chain-based viral gene prediction program
(http://www.softberry.com). Splice sites were determined manually ...
The ISME Journal
6, 915-926 (May 2012) | doi:10.1038/ismej.2011.169
Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome
Pride et al.,
... Viral contigs were analyzed using FGenesV (Softberry Inc., Mount Kisco, NY, USA) for open
reading frame prediction, and individual Open reading frames were analyzed using blastX analysis
against the NCBI non-redundant database (E-score <10 ?5 ). If the best hit was to a ...
Virology Journal
2011, 8:331
http://www.virologyj.com/content/8/1/331
The complete genome sequence and genetic
analysis of fFCA82 a novel uncultured
microphage from the turkey gastrointestinal
system
Zsak et al.,
1
Southeast Poultry Research Laboratory, Agricultural Research Service, United
States Department of Agriculture, 934 College Station Road, Athens, GA
30605 USA
...Putative ORFs
within the FCA82 genome were predicted using the FGENESV Trained Pattern/Markov chain-based viral gene prediction method from the Softberry website [27]....
Aquat Biol
Vol. 14: 223–232, 2012 doi: 10.3354/ab00395
Genetic diversity of the Caribbean spiny lobster virus, Panulirus argus virus 1 (PaV1), and the discovery of PaV1 in lobster postlarvae
Jessica Moss 1, *, Mark J. Butler IV 2 , Donald C. Behringer 3 , Jeffrey D. Shields 1
1
Department of Environmental and Aquatic Animal Health, Virginia Institute of Marine Science, Greate Road,
Gloucester Point, Virginia 23062, USA
2
Department of Biological Sciences, Old Dominion University, Norfolk, Virginia 23529, USA
... FgenesV (http:// linux1. softberry. com/), a trained pattern/Markov chain-based viral gene
prediction program, was used to translate the sequenced region and to identify ORFs or
possible viral genes. RESULTS PaV1 detection by PCR Postlarvae ...
PLoS ONE
(2011), 6(11): e28163. doi:10.1371/journal.pone.0028163
Genomic Sequence Analysis of Granulovirus Isolated from the Tobacco Cutworm, Spodoptera litura.
Wang et al.,
Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
...Putative coding regions of the SpliGV genome were predicted using FGENESV0 (http://www.softberry.com/berry.phtml) [70] and the ...
Virology
Volume 414, Issue 1, 25 May 2011, Pages 42–50 DOI: 10.1016/j.virol.2011.03.009
Deep sequencing of Cotesia vestalis bracovirus reveals the complexity of a polydnavirus genome
Chen et al.,
a State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310029, China
b Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China
...Putative open reading frames (ORFs) were predicted using FGENESV (http://linux1.softberry.com/berry.phtml) and GENSCAN...
J Gen Virol
November 2011 vol. 92 no. 11 2679-2690 DOI: 10.1099/vir.0.033852-0
The enigmatic genome of Chara australis virus
Gibbs et al.,
Research School of Biological Science, Australian National University, Canberra, ACT 0200, Australia
...ORFs were predicted by using the MolQuest-Softberry viral gene detector, ...
PLoS ONE
5(1): e8812. doi:10.1371/journal.pone.0008812
Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community
Allgaier et al.,
1 Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America, 2 Department of Biological and Agricultural Engineering, University of California Davis, Davis, California, United States of America
.. scores. After manual frameshift correction, genes were called using fgenesb
(http://www.softberry.com). For ... Iodobacteriophage. Genes were predicted using fgenesV
(www.softberry.com). (1.12 MB EPS). Figure S2. Correspondence ...
Journal of Insect Physiology
Volume 56, Issue 6, June 2010, Pages 650-658 doi:10.1016/j.jinsphys.2010.01.013
Transient expression of specific Cotesia plutellae bracoviral segments induces prolonged larval development of the diamondback moth, Plutella xylostella
Bowon Kwon a, c, Seongbaeck Song a, Jae Young Choi b, Yeon Ho Je b and Yonggyun Kim a
a Department of Bioresource Sciences, Andong National University, Andong 760-749, Republic of Korea
b Department of Entomology, Seoul National University, Seoul 151-742, Republic of Korea
... Putative genes encoded in the CpBV genome segments were analyzed by FGENESV ORF Finder
(http://linux1.softberry.com/berry.phtml?topic=index&group=programs&subgroup=gfindv) and
NCBI-BLAST searching programs, in which genes were predicted by two criteria that ...
PLoS Pathog
2010 6(5): e1000923. doi:10.1371/journal.ppat.1000923
Analysis of Virion Structural Components Reveals Vestiges of the Ancestral Ichnovirus Genome
Volkoff et al.,
1 UMR 1231 INRA - Universite Montpellier 2, Biologie Integrative et Virologie des Insectes, Place Eugene Bataillon, Montpellier, France, 2 Institut de Genomique Fonctionnelle, Plate-forme Proteomique, CNRS UMR 5203, INSERM U661, Universite Montpellier 1, Universite Montpellier 2, Montpellier, France
... Five related sequences, showing more than 65% nucleotide identity, are highlighted. Arrows
represent the predicted coding sequences in IVSPER-2 (names as per Figure 1) and CsIV
SH-C (as determined using FGENESV0 at http://linux1.softberry.com/berry.phtml). ...
Archives of Virology
Volume 154, Number 8 / August 2009, pp. 1313-1327
Sequence and gene organization of 24 circles from the Cotesia plutellae bracovirus genome
Jae Young Choi et al.,
(1) Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Korea
... specific primers. For each genomic segment, putative coding genes were predicted
using FGENESV0 (http://www.softberry.com/berry.phtml) [48] and GENSCAN
(http://genes.mit.edu/GENSCAN.html). Sequence comparisons ...
Virus Research
Volume 132, Issues 1-2, March 2008, Pages 132-139 doi:10.1016/j.virusres.2007.11.009
Completion of the genome analysis of snake adenovirus type 1, a representative of the reptilian lineage within the novel genus Atadenovirus
SL Farkas, B Harrach, M Benko
Veterinary Medical Research Institute, Hungarian Academy of Sciences, H-1581, Budapest, P.O. Box 18, Hungary
... The complete genome sequence was also submitted to the FGENESV program at
www.softberry.com (Softberry Inc.) for putative gene prediction. ...
Entomological Research
Volume 38 Issue 1 Page 77-86, March 2008
Differential expression profile of genes encoded in a genome segment of Cotesia plutellae bracovirus in a parasitized host, Plutella xylostella
Wael GAD, Jae Young, Yeon Ho JE, Yonggyun KIM
1 Department of Bioresource Sciences, Andong National University, Andong, Korea
2 School of Agricultural Biotechnology, Seoul National University, Seoul, Korea
... Putative open reading frames (ORF) were predicted using fgenesv0 (Solovyev & Salamov
1999; http://www.softberry.com/berry.phtml) and genescan (http://genes.mit ...
Archives of Virology
Volume 152, Number 11 / October 2007 p. 2027-2033
Identification, detection and transmission of a new vitivirus from Mentha
I. E. Tzanetakis, J. D. Postman and R. R. Martin
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, U.S.A.
... Genome analysis The open reading frames (ORF) encoded by MV-2 were identified with
the FGENESV0 and ORF finder programs (http:==www.softberry.com and http:==www ...
Journal of Virology
July 2007, p. 6920-6926, Vol. 81, No. 13
Detection of a Novel and Highly Divergent Coronavirus from Asian Leopard Cats and Chinese Ferret Badgers in Southern China
B. Q. Dong et al.,
Guangxi Center for Disease Control and Prevention
... Open reading frames (ORFs) of the partial genome of the novel CoV were identified
with the program fgenesV (Softberry Inc., Mount Kisco, NY) and mapped with ...
J Gen Virol
87 (2006), 1531-1541;
Comparative genomic analysis of two strains of human adenovirus
type 3 isolated from children with acute respiratory infection in southern China
Qiwei Zhang et al.,
State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
... or 'hypothetical proteins' were also identified by using FGENESV, software for
predicting potential genes in viral genomes (http://www.softberry.com/berry ...
Journal of Virology
March 2006, p. 2127-2140, Vol. 80, No. 5
Vaccinia Virus Proteome: Identification of Proteins in Vaccinia Virus Intracellular Mature Virion Particles
Che-Sheng Chung,1, Chein-Hung Chen,2, Ming-Yi Ho,2 Cheng-Yen Huang,1 Chung-Lin Liao,2* and Wen Chang1*
Institute of Molecular Biology,1 The Genomics Research Center, Academia Sinica, Taipei, Taiwan, Republic of China2
... predicted from WR viral genome sequences using two programs, GeneMarkS
(http://opal.biology.gatech.edu/GeneMark/) and fgenesV (http://softberry.com; 17). ...
Biochem Biophys Res Commun.
2005 Jul 1;332(2):487-93.
Genomic segments cloning and analysis of Cotesia plutellae polydnavirus using plasmid capture system
Choi et al.,
School of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Republic of Korea.
... Putative coding regions were predicted using FGENESV0 ([21]; http://www.softberry.
com/berry.phtml) and GENSCAN (http://genes.mit.edu/GENSCAN.html). ...
Journal of Asia-Pacific Entomology
2005, v. 8(4) p. 359-366
Structure and Expression Profiles of Two Putative Cotesia plutellae Bracovirus Genes (CpBV-H4 and CpBV-E94?) in Parasitized Plutella xylostella
MA Ibrahim Ahmed, et al.,
Andong National University, Andong, Republic of Korea
... Puta- tive ORFs were predicted using FGENESV0 (Solovyev and Salamov, 1999:
http://www.softberry. com/berry. phtml) and GENSCAN (http://genes.mit. edu/ GENSCAN. ...
Journal of Asia-Pacific Entomology
2005, v. v. 8(3) p. 249-255
Gene Expression of Cotesia plutellae Bracovirus EP1-like Protein (CpBV-ELP1) in Parasitized Diamondback Moth, Plutellae xylostella
Lee, et al.,
Andong National University, Andong, Republic of Korea
... Puta- tive ORFs were predicted using FGENESV0 (Solovyev and Salamov, 1999:
http://www.softberry. com/berry. phtml) and GENSCAN (http://genes.mit. edu/ GENSCAN. ...
Virus Research
Volume 112, Issues 1-2, September 2005, Pages 32-37
New features in the genus Ilarvirus revealed by the nucleotide sequence of Fragaria chiloensis latent virus
Ioannis E. Tzanetakis a and Robert R. Martin a, b,
aDepartment of Botany and Plant Pathology, Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331, USA
bHorticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR 97330, USA
... that position of FClLV RNA 2. An ORF at an alternative reading frame was identified
(Pattern/Markov chain-based viral gene prediction at softberry.com) between ...
Archives of Virology
Volume 149, Number 10 / October, 2004 pp. 2001-2011
Strawberry necrotic shock virus is a distinct virus and not a strain of Tobacco streak virus
I. E. Tzanetakis, I. C. Mackey and R. R. Martin
Molecular and Cellular Biology Program and Department of Botany and Plant Pathology,
Oregon State University, Corvallis, OR, U.S.A.
USDA-ARS, HCRL, Corvallis, OR, U.S.A.
... similarity to any gene in the database and this was predicted not to be
a virus-encoding gene sequence (Virus gene identification, www.softberry.com ...
Journal of Virology
November 2004, p. 12576-12590, Vol. 78, No. 22
Functional Genomics Analysis of Singapore Grouper Iridovirus: Complete Sequence Determination and Proteomic Analysis
Wen Jun Song,1 Qi Wei Qin,2 Jin Qiu,1 Can Hua Huang,1 Fan Wang,1 and Choy Leong Hew1*
Department of Biological Sciences,1 Tropical Marine Science Institute, National University of Singapore, Singapore2
... A total of 162 ORFs, predicted by the FGENESV program (available through:
http://www.softberry.com), supplemented with Vector NTI suite 7.1, are indicated ...
Virus Genes
28 (3): 239-246, April 2004
Article ID: 5269250
Complete Nucleotide Sequence of a Strawberry Isolate of Beet Pseudoyellows Virus
Ioannis E. Tzanetakis
Molecular and Cellular Biology Program, Department of Botany and Plant Pathology,
Oregon State University, Corvallis 97331, USA
Robert R. Martin
Horticultural Crops Research Laboratory, USDA-ARS, Corvallis OR 97330, USA;
... http://www.ncbi.nlm.nih. gov/gorf/gorf.html) and the gene finder in viruses at http://www.softberry.com. The amino acid comparisons ...
Geno., Prot. & Bioinfo.
Vol. 1 No. 3 August 2003 226-235
Genome Organization of the SARS-CoV
Jing Xu1* et al
1 Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
...FGENESV, a program for gene prediction provided by Softberry Inc. (Mount Kisco, USA) through a web-based interface, has been specially modi?ed and trained with parameters for virus (http://www.softberry.com/berry.phtml?topic= gfindv).
...
The hypothetical minus sense ORF iden-ti?ed by FGENESV (from 48 to 203 nt on the minus strand or 29,523 to 29,678 nt on the plus strand) may be fake, but we should not absolutely deny the prob-ability of the existence of minus ORFs.
...Furthermore, we employed FGENESV to explore the sequences of MHV (NC 001846 in NCBI) and AIBV (NC 001451 in NCBI), and compared the re-sults with their previous annotations, respectively.
Rapport de stage de DEA Juin 2003
Analyse du genome du virus de l'archee Pyrococcus abyssi (PAV1)
ROUAULT Karen
Laboratoire de Microbiologie et Biotechnologie des Extremophiles IFREMER- Centre de Brest et Equipe Microbiologie LEMAR - Institut Universitaire Europeen de la Mer
... [14]. FGENESV http://www.softberry.com/berry. phtml?topic=gfindv Virus ( >10
kb) Modeles de Markov Forme du genome Code genetique [40]. ...
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