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HIV sequence database

Gene Cutter

Sequence Alignment and Protein Extraction

Purpose: Gene Cutter is a sequence alignment and protein extraction tool for HIV-1, HIV-2 or SIV. This tool will:

  • Align your nucleotide sequences (if they aren't already aligned).
  • Clip coding regions from a nucleotide alignment.
  • Codon-align all coding regions.
  • Generate nucleotide and protein alignments of the cut regions.

Please read Gene Cutter Help, particularly before running large jobs.

Paste your sequences
[Sample Input]
Or upload your file
Check if appropriate
Sequences are unaligned icon
Region(s) to align and extract icon
Reference options
Insert HXB2(K03455) for HIV-1 or SMM239(M33262) for HIV-2/SIV into the results icon
Remove HXB2(K03455) for HIV-1 or SMM239(M33262) for HIV-2/SIV from the results icon
Check if appropriate
Codon align the region icon     Allow codons to compensate frameshift
Output format Translate to amino acids:
Codons containing an IUPAC character shown as "X" icon
Codons containing an IUPAC character in a silent position translated; others shown as "X" icon
Codons containing an IUPAC character translated icon
Return results as nucleotides:
Do not translate

Please be patient. Do not resubmit your sequences; you will not get a result any faster, and you will load up our server and make the process slower. If you don't receive your results within a reasonable time, check the link in your "job started" e-mail and/or contact us.

last modified: Wed Sep 19 16:17 2018

Questions or comments? Contact us at

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