Purpose: Find the HIV database sequences most similar to your query(s).
Details: Our DNA database contains most of the same HIV sequences found in GenBank, but a BLAST search here gives more informative output. The results will contain some of the fields we annotate, such as subtype, sampling country and isolation year.
Input: One nucleotide or amino acid sequence, or a bulk set of sequences. A single sequence can be in FastA format or raw sequence.
Bulk input: A bulk set may be submitted in FastA or any common sequence format; the sequences do not need to be aligned. Bulk input is limited to 100 sequences and <500 Kb file size. A maximum of 10 matches will be displayed per query. To enter multiple accession numbers, separate each by space or comma. For large sets, we recommend that you uncheck "Show location of match in genome", as the results may take hours if this is included.
See HIV BLAST Examples for examples of 'Pairwise' and 'Master-Slave' output.
Run BLAST against:
The default BLAST background is all sequences in the LANL HIV Database.
You can also search only the sequences with assigned subtypes, or sequences of one pure subtype.
If you want to BLAST against your own submitted background set, browse for a file that contains those sequences.
Subsequent analyses: From the BLAST results page, you can:
References: BLAST references