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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
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
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: Fri Mar 4 11:01 2016

Questions or comments? Contact us at

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