Literature DB >> 10871272

Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes.

D Hiscock1, C Upton.   

Abstract

SUMMARY: The Viral Genome DataBase (VGDB) contains detailed information of the genes and predicted protein sequences from 15 completely sequenced genomes of large (&100 kb) viruses (2847 genes). The data that is stored includes DNA sequence, protein sequence, GenBank and user-entered notes, molecular weight (MW), isoelectric point (pI), amino acid content, A + T%, nucleotide frequency, dinucleotide frequency and codon use. The VGDB is a mySQL database with a user-friendly JAVA GUI. Results of queries can be easily sorted by any of the individual parameters. AVAILABILITY: The software and additional figures and information are available at http://athena.bioc.uvic.ca/genomes/index.html .

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Year:  2000        PMID： 10871272     DOI： 10.1093/bioinformatics/16.5.484

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  12 in total

1.  Poxvirus orthologous clusters: toward defining the minimum essential poxvirus genome.

Authors:  Chris Upton; Stephanie Slack; Arwen L Hunter; Angelika Ehlers; Rachel L Roper
Journal:  J Virol       Date:  2003-07       Impact factor: 5.103

2.  National center for biotechnology information viral genomes project.

Authors:  Yiming Bao; Scott Federhen; Detlef Leipe; Vyvy Pham; Sergei Resenchuk; Mikhail Rozanov; Roman Tatusov; Tatiana Tatusova
Journal:  J Virol       Date:  2004-07       Impact factor: 5.103

Review 3.  Unraveling the web of viroinformatics: computational tools and databases in virus research.

Authors:  Deepak Sharma; Pragya Priyadarshini; Sudhanshu Vrati
Journal:  J Virol       Date:  2014-11-26       Impact factor: 5.103

4.  Phosphorylation of yellow fever virus NS5 alters methyltransferase activity.

Authors:  Dipankar Bhattacharya; Spencer Hoover; Shaun P Falk; Bernard Weisblum; Martha Vestling; Rob Striker
Journal:  Virology       Date:  2008-08-30       Impact factor: 3.616

5.  VirGen: a comprehensive viral genome resource.

Authors:  Urmila Kulkarni-Kale; Shriram Bhosle; G Sunitha Manjari; A S Kolaskar
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

6.  Improving gene annotation of complete viral genomes.

Authors:  Ryan Mills; Michael Rozanov; Alexandre Lomsadze; Tatiana Tatusova; Mark Borodovsky
Journal:  Nucleic Acids Res       Date:  2003-12-01       Impact factor: 16.971

7.  Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource.

Authors:  Elliot J Lefkowitz; Chris Upton; Shankar S Changayil; Charles Buck; Paula Traktman; R Mark L Buller
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

8.  VIDA: a virus database system for the organization of animal virus genome open reading frames.

Authors:  M M Albà; D Lee; F M Pearl; A J Shepherd; N Martin; C A Orengo; P Kellam
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

9.  Functional genomics as a tool in virus research.

Authors:  Ruchi Ratra; Sunil K Lal
Journal:  Indian J Microbiol       Date:  2008-07-27       Impact factor: 2.461

10.  From protein interactions to functional annotation: graph alignment in Herpes.

Authors:  Michal Kolár; Michael Lässig; Johannes Berg
Journal:  BMC Syst Biol       Date:  2008-10-28
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