HCV Database
HCV sequence database

To our users Please note that the HCV database site is no longer funded. We try to keep the database updated and the tools running, but unfortunately, we cannot guarantee we can provide help for using this site. Data won't be manually curated either.

Gene Cutter

Sequence Alignment and Protein Extraction

Purpose: Gene Cutter is a sequence alignment and protein extraction tool for HCV. 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
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.

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