Comparative Analysis of Virus Sequences
Currently more than 600 complete virus genomes are available in the
public sequence repository GenBank. Sequence comparison methods allow
us to identify protein regions that have been conserved in proteins
that have a common ancestor (homologues). These conserved regions
generally represent functionally important domains. However homology
relationships between proteins are not explicitly mapped in primary
databases such as GenBank and, more specialised, secondary, databases
are required. We have developed a database that organises virus
protein sequences into homologous protein families, automatically
identifies conserved sequence domains in the proteins and uses a
consistent system to organise virus functions and taxonomic
Virus Database (VIDA)
also includes links to other databases such as PDB, CATH and Swissprot. In
VIDA all available sequences from the herpesvirus, poxvirus,
arterivirus, coronavirus and papillomavirus can be examined. The
homologous protein families have also been used for herpesvirus
phylogeny reconstruction on the basis of gene content and to annotate
clusters of genes derived from array-based mRNA quantitation
- M.M. Albà, D. Lee, F.M.G. Pearl, A.J. Shepherd, N. Martin, C.A. Orengo and P. Kellam.
"VIDA: A virus database system for the organization of virus genome open reading frames."
Nucleic Acids Research, 29:133-136 (2001).
- M.M. Albà, R. Das, C. Orengo and P. Kellam.
"Genome wide function conservation and phylogeny in the Herpesviridae."
Genome Research, 11:43-54 (2001).
- R. Jenner, M.M. Albà, C. Boshoff and P. Kellam.
"Kaposi's sarcoma-associated herpesvirus latent and lytic gene expression as revealed by DNA arrays."
Journal of Virology, 75:891-902 (2001).