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 has a few problems, and it is unlikely that they can be fixed in the near future. We are working on a tool that we hope will replace it: HCValign. Please give this a try if you have trouble getting Gene cutter to work.

Gene Cutter is a versatile tool that can:
  • align your nucleotide sequences
  • codon align the coding regions, so they can be readily translated
  • clip pre-defined (coding) regions from a nucleotide alignment
  • generate nucleotide and protein alignments of the cut regions
  • provide alternate translations for codons with ambiguity codes
  • accept and automatically detect the following input formats:
  • Clustal EMBL Fasta GCG
    GDE GenBank Mase MEGAs
    MEGAi MSF NEXUSi NEXUSs
    Phylips Phylipi PIR RSF
    SLX RAW Stockholm Table
Gene cutter now accepts unaligned sequences and aligns them, and it does not require the H77 reference sequence to be included in the input nucleotide alignment. Note about email result notification: If H77 is not in your submitted sequences, you are submitting more than 100 sequences, or you check Align sequences below, the next page will ask you for your email address and you will be notified when your output is ready.

More on Gene Cutter's workings and possibilities is here.

How to use: GeneCutter attempts to automatically recognize the format of your input file, using Format Conversion. If this fails, you can use the Sequence Conversion Tools interface to convert your alignment to fasta, and use that for input.

Input
Paste your input here
[SAMPLE INPUT]
Or upload your file

Options
Align sequences
Codon-align sequences
Region to extract
Output format
Translate to amino acids No
Yes



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