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. It can be used for any set of nucleotide sequences for HCV.

Gene Cutter can:

  • align your nucleotide sequences (if they aren't already aligned)
  • clip pre-defined coding regions from a nucleotide alignment
  • codon-align the coding regions
  • generate nucleotide and protein alignments of the cut regions

Details: The reference sequence used by this tool is H77. Gene coordinates are based on these reference sequences. This version of Gene Cutter doesn't require a reference sequence to be included in your input nucleotide alignment. Gene Cutter will also accept unaligned sequence sets. Gene Cutter uses Hmmer with a training set of the full-length genome alignment and will give a better multiple alignment than many computationally-based alignment programs. Misalignments at the ends of a coding region may result in a few amino acids/bases not appearing in the output for that coding region.

In some sequences, an insertion will be compensated within a short distance by a deletion, or vice versa. As these frameshifts may not inactivate the protein, if a compensating mutation is within 5 amino acids of an initial frameshift, the shifted reading frame is left intact. Otherwise, the frame shift is marked with the hash symbol (#), and the translation is continued in the correct reading frame beyond the offending codon. Stop codons are marked by a dollar sign ($).

The best results will be obtained if you submit an alignment that has been hand-aligned and contains the correct reference sequence. For more information, see Gene Cutter Explanation.

Input
Paste your sequences
[Sample Input]
Or upload your file:
Check box if appropriate Sequences are unaligned

Options
Region(s) to align and extract
Codon align the region

Translation options
Codons containing an IUPAC character are shown as "X".
Codons containing an IUPAC character in a silent position are translated; others are shown as "X".
Codons containing an IUPAC character are translated.
Do not translate to amino acids
Note: codons containing "-" are always translated to either "-" (gap) or "#" (partial codon)

Please be patient. Your input file must download to our server, where the actual work is performed. This can take several minutes. 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.




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