HIV Databases HIV Databases home HIV Databases home
HIV sequence database
Development



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.

Input
Organism
Paste your sequences
[Sample Input]
Or upload your file
Check if appropriate Sequences are unaligned icon
Options
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: Thu Jan 21 13:19 2016


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

 
Operated by Los Alamos National Security, LLC, for the U.S. Department of Energy's National Nuclear Security Administration
Copyright © 2005-2012 LANS LLC All rights reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health