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Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database

R W Shafer1, D Stevenson, B Chan

  • 1Division of Infectious Diseases, Stanford University Medical Center, Stanford, CA 94305, USA. rshafer@cmgm.stanford.edu

Nucleic Acids Research
|December 10, 1998
PubMed
Summary
This summary is machine-generated.

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The HIV Sequence Database provides a comprehensive resource for human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease sequences. It links genetic data with drug resistance and treatment history for research.

Area of Science:

  • Virology
  • Bioinformatics
  • Genetics

Background:

  • Human immunodeficiency virus (HIV) exhibits significant genetic variation in its reverse transcriptase (RT) and protease enzymes.
  • This variation is crucial for understanding viral evolution and the development of drug resistance.
  • Access to curated sequence data linked with clinical information is essential for effective HIV research and treatment strategies.

Purpose of the Study:

  • To establish and maintain a comprehensive online relational database of HIV RT and protease sequences.
  • To link viral sequence data with critical information on drug treatment history and isolate source.
  • To facilitate research into HIV evolution, drug resistance, and subtype diversity.

Main Methods:

  • Compilation of nearly all published HIV RT and protease sequences from diverse sources (e.g., GenBank, journal articles).

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  • Integration of sequence data with detailed information on patient treatment history and sample origin.
  • Annotation of sequences using data from 180 literature references and expert curation.

    • Main Results:

    • Creation of a centralized, searchable online database (http://hivdb.stanford.edu) cataloguing HIV RT and protease sequences.
    • Enrichment of sequence data with extensive metadata, including drug resistance profiles and viral subtypes.
    • Development of tools for users to retrieve specific sequence sets and perform alignments based on defined criteria.

    Conclusions:

    • The HIV RT and Protease Sequence Database serves as a vital resource for the scientific community.
    • It enables in-depth analysis of HIV sequence variation in relation to treatment outcomes and evolutionary patterns.
    • The database supports the ongoing development of improved HIV diagnostics, therapeutics, and preventative strategies.