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.


HCV BLAST

Purpose: Find the HCV database sequences most similar to your query(s).

Input
Paste your sequence(s)
[Sample Input]
or upload a file
or enter accession number(s)

Options
Output style See examples.
Number of BLAST matches to display
Run BLAST against
or a background set of sequences you upload
E-mail Always email results
Show location of match in genome Only matters for nucleotide input; uncheck to speed the job

Details: Our DNA database contains most of the same HCV sequences found in GenBank, but a BLAST search here gives more informative output. The results will contain some of the fields we annotate, such as subtype, sampling country and isolation year.

Input: One nucleotide or amino acid sequence, or a bulk set of sequences. A single sequence can be in FastA format or raw sequence.

Bulk input: A bulk set may be submitted in FastA or any common sequence format; the sequences do not need to be aligned. Bulk input is limited to 100 sequences and <500 Kb file size. A maximum of 10 matches will be displayed per query. To enter multiple accession numbers, separate each by space or comma. For large sets, we recommend that you uncheck "Show location of match in genome", as the results may take hours if this is included.

Output style: See HCV BLAST Examples for examples of 'Pairwise' and 'Master-Slave' output.

Run BLAST against: The default BLAST background is all sequences in the LANL HCV Database. You can also search only the sequences with assigned genotypes, or sequences of one pure genotype. If you want to BLAST against your own submitted background set, browse for a file that contains those sequences.

Subsequent analyses: From the BLAST results page, you can:

  • Download and align all or a selection of your output sequences,
  • Use the Geography search to examine the origin of your BLAST results,
  • Run NCBI BLAST.

References: BLAST references




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