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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.

New! Have multiple sequence files and want to submit them as multiple jobs all at once? use Gene Cutter-B
Want to call GeneCutter in a commandline or in your script? use SimpleGC

Paste your sequences
[Sample Input]
(Manually edited alignments containing a correct reference sequence will have best results)
Or upload your file
Input sequences are pre-aligned icon
Region(s) to align and
Reference options
  HIV-1: HXB2(K03455), HIV-2/SIV: MAC239(M33262)
Insert the reference sequence into the results, if not included in your input icon
Remove the references originally included in your input from the results icon
Codon align 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
Email results

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: Thu Sep 26 13:20 2019

Questions or comments? Contact us at

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