Affiliations: MedImmune, Inc., 297 N. Bernardo Ave., Mountain View,
CA 94043, USA. Tel.: +1 650 603 2446; E-mail: yanq@medimmune.com
Abstract: Viruses are major factors of human infectious diseases.
Understanding of the structure-function correlation in viruses is important for
the identification of potential anti-viral inhibitors and vaccine targets. In
virology research, virus-related databases and bioinformatic analysis tools are
essential for discerning relationships within complex datasets about viruses
and host-virus interactions. Bioinformatic analyses on viruses include the
identification of open reading frames, gene prediction, homology searching,
sequence alignment, and motif and epitope recognition. The predictions of
features such as transmembrane domains, glycosylation sites, and protein
secondary and tertiary structure are important for analyzing the
structure-function relationship of proteins encoded in viral genomes.
Biochemical pathway analysis can help elucidate information at the biological
systems level. Microarray analysis provides methods for high throughput
screening and gene expression profiling. Virus-related bioinformatics databases
include those concerned with viral sequences, taxonomy, homologous protein
families, structures, or dedicated to specific viruses such as influenza and
herpes simplex virus (HSV). This review provides a guide and overview of
computational programs for these analyses as a resource for genomics and
proteomics studies in virology research. These resources are useful for
understanding viral diseases, as well as for the design and development of
anti-viral agents.
