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Bioinformatics Vol. 16 no. 5 2000
Pages 484-485
© 2000 Oxford University Press

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

David Hiscock 1 and Chris Upton 1,*

1 Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055, Victoria, BC V8W 3P6, Canada

Received on August 24, 1999 ; revised on November 16, 1999 ; accepted on January 8, 2000

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.

Contact: cupton{at}uvic.ca

* To whom correspondence should be addressed.


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