HIV BLAST Search

Purpose: HIV BLAST finds the database sequences most similar to your query.

Details: Although our DNA database contains mostly the same HIV sequences found in GenBank, doing the search here gives a more informative output. The output list will contain some of the fields we annotate, such as subtype, sampling country, isolation year, and the genomic location of the sequence alignment.

Note that results are listed by score, and score is not always correlated with percent identity. For example, if you BLAST a full-length sequence, the top scores will be other full-length sequences; shorter sequences of higher identity will be missed.

Input options: One nucleotide sequence or 1 amino acid sequence may be submitted per run. The sequence can be submitted in FastA format or as raw sequence. The sequence can be submitted by pasting into the text area, browsing for a file containing the sequence, or specifing a GenBank accession number.

Background options: The default is to BLAST your query against all sequences in the HIV Database. If you want to BLAST against your own submitted background set, browse for a file that contains those sequences in the space provided below.

Output options: You can download all or a selection of the sequences your BLAST search finds. If you choose the 'master-slave' output option the downloaded sequences will be aligned to one another. If you choose 'pairwise' the downloaded sequences will not necessarily be aligned.

Help files:
HIV BLAST Output Examples: examples of 'master-slave' and 'pairwise' output.
BLAST references