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

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. Contact: cupton@uvic.ca