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HIV sequence database



HIV BLAST

Purpose: Find the HIV database sequences most similar to your query(s).

Input
Paste your sequence(s)
or upload a file
or enter accession number(s)

Options
Output style See examples.
Number of BLAST matches to display
Run BLAST against
or a background set of sequences you upload
E-mail Always email results
Show location of match in genome Only matters for nucleotide input; uncheck to speed the job

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.

Output style: 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:

  • Download and align all or a selection of your output sequences,
  • Use the Geography search to examine the origin of your BLAST results,
  • Run NCBI BLAST.

References: BLAST references

last modified: Thu Apr 11 11:16 2013


Questions or comments? Contact us at seq-info@lanl.gov.

 
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