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.


VirAlign for HCV sequences

Purpose: HCValign takes aligned or unaligned nucleotide sequences and gives the alignment of the region which the input sequences touched. If your sequences aren't pre-aligned, this tool can align them via a Hidden Markov Model or MAFFT.

Usage: Paste your sequence(s) into the space provided, or browse for your file. Then you may choose options.

Explanation: Please read the Explanation below before using.

Paste your sequence(s)
Or upload your sequence file
Select feature

Always e-mail result
Align the sequences       By HMM-align     By MAFFT
Codon-Align the sequences        Allow codons to compensate frameshift
Insert a reference sequence        H77
Translate to amino acid

Note: This program is computationally intensive and may take a while to run. Please don't resubmit your request!

Explanation: HCValign aligns input sequences to a reference sequences and clips the regions the input touched. There are five options:

HCValign attempts to automatically recognize the format of your input file by using Format Converter. The results page summarizes the running parameters and information about the input, and gives you the alignment of the region which the input touched . From this page you can download the alignment in different formats, or send the resulting alignment to TreeMaker or FindModel.

Aligning large sequences is a computationally intensive procedure. An input file that is pre-aligned and smaller than 500 Kb is run immediately. If your input file exceeds the limit, or if you checked the 'Align' option , your job will be run in batch, and you will receive an email when it has finished. The email contains link to your results.


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