Vida bsm/virus_database/VIDA.html

Homologous protein families from herpes, pox, papilloma, corona-viruses, and arteriviruses

Subviral RNA cgi-bin/home.cgi

Sequences and prediction of RNA secondary structures

One of the promising sources of sequence information for viruses is the Viral Genomes Project, involving the National Center for Biotechnology Information (NCBI) at the National Institutes of Health, USA. The URL for the database is (for reviews see Refs. [10, 11]). The reasons for creating the Viral Genomes Project have been the increasing number of viral nucleotide sequences deposited in data banks, uncertain quality of some of the early sequences, and the great variability of viral genomes. This variability has two distinct manifestations: the different types of nucleic acid structures (DNA or RNA, single-stranded or double-stranded, linear or circular, segmented or unsegmented), and the great variation in genomic nucleotide sequences among viruses generally and also within individual, taxono-mically defined viruses [12].

Genetic heterogeneity and potential for rapid evolution reach their maximum manifestation in the quasispecies structure of RNA viruses, in which a distribution of mutants constitutes what was classically called the "wild type" virus (implications of quasispecies for data banks are discussed in Section 17.4). Extreme diversity in genome structure and the presence of mutant spectra in a majority of viral isolates complicates sequence records and may cause inaccuracies in the transfer of information to data banks [10].

Complete sequencing of complex viral genomes has prompted the development of virus-specific or viral family databases that differ in format and contents, and that may include phenotypic traits derived from sequence information; for example, RNA structure predictions (reviewed in several chapters of Refs. [13] and [7]), mutations related to antiviral drug resistance, etc. The construction of homologous protein families (HPFs) is also a feature included in some databases, allowing insight in virus protein functions. As an example, the VIDA database contains a collection of HPFs derived from open reading frames from complete and partial virus genomes [14].

0 0

Post a comment