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HIV Sequence Database


NAR Molecular Biology Database Collection entry number 76
Leitner, T., Foley, B., Hahn, B., McCutchan, F., Marx, P., Wolinsky, S., Mellors, J., Moore, J., Korber, B.
Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Contact tkl@lanl.gov

Database Description

The HIV Sequence Database contains all published and many unpublished HIV and related SIV DNA and translated amino acid sequences. Currently, >95,000 entries are maintained and annotated. The database is fully searchable through several search tools and contains many tools for sequence analysis.

The search tools include an interface where sequences are searchable through accession number, name, sampling country, subtype, sampling year, risk factor, coreceptor usage, phenotype and more. Another search tool uses geographic subtype distributions. The search results are presented as tables covering important sequence information and the sequences can be downloaded as multiple pairwise alignments. Some examples among the many tools are: Gene Cutter that clips pre-defined coding regions from a nucleotide alignment, then codon aligns and provides translations of the cut regions, Seq-Covert that converts between different formats, Primalign that aligns your primer or sequence fragment to the complete genome alignment, the HIV/SIV Sequence Locator that finds the position of your nucleotide or protein sequence in HIV relative to a reference, RIP that performs a recombination analysis, Hypermut that can detect hypermutated sequences, SNAP that calculates synonymous and non-synonymous substitutions, PCoord that summarizes variation among sequences in ten 'dimensions' where each sequence gets a score on each of these dimensions, and HIV-BLAST that performs a BLAST search on HIV sequences. Some simple tree building interfaces are present and more advanced and versatile tree tools are currently being developed.

The database also provides alignments of all full length HIV and SIV genomes, consensus and reconstructed ancestral sequences, and reference sequences for subtyping, recombination analyses and other purposes.

In addition, the database publishes a yearly hard copy compendium with selected sequences and review articles on recent developments in HIV genetic research. These reviews and additional tutorials on sequence analysis are also available on the web site.

Subcategory: Viral genome databases

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