ABSTRACT: Objectives: HIV reverse transcriptase (RT) and protease sequences and drug susceptibility data are published in journals, meeting abstracts and GenBank. However, data in these formats are often not useful for subsequent analyses and may not even be adequate for effective peer review. HIV RT and protease sequence database (http://hivdb.stanford.edu; Nucleic Acids Research 1999; 27:348-352) is a publicly available database that catalogues evolutionary and drug-related HIV RT and protease sequence variation. We will present a live demonstration of the database with an emphasis on features added in 1999.
Methods: The database contains curated sequences, drug susceptibility results and HIV drug treatment histories linked to approximately 5000 HIV isolates and is annotated with >300 literature references. Normalized data reside in a relational database; ASP and CGI programming provide the web interface.
Results: There have been three database additions in 1999: (i) The schema was extended to include drug susceptibility data; (ii) derived data sets (data warehouse) have become the primary source for queries; and (iii) an interactive program, HRPSeq, analyses user-submitted sequences in the context of published RT and protease sequence data.
Conclusions: The integration of experimental results in a standardized format makes such data amenable to ongoing scrutiny and subsequent additional analyses. With its recent changes, the HIV RT and protease sequence database is evolving from an archival database into one that meets the data requirements of a growing number of users and undertakes to develop a coherent model of the genetic mechanisms underlying HIV drug resistance.
