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.


Example: "Ambiguity" Gap Strip

Goal: Your alignment contains IUPAC ambiguity codes "r" meaning A or G, and "y" meaning C or T. You want to remove all columns from your alignment that contain one or more of the ambiguity codes and one or more gaps.

Data: The alignment in the box below contains ambiguity code "r" column 1, and "y" in column 7. There are also gaps in various columns.

Settings: The tolerance for gaps is set to zero, and in addition r and y are entered as gap characters in the "gap characters" box. Columns 1, 2, 4, and 7 will be removed when you press the Run button.

Alignment:

Options:

Gap character(s)

Tolerance for gaps (%)

Show deleted columns

Preserve codons (delete columns in groups of 3)

Use tolerance for [1,2,3]
positions in the codon:

Reading frame of alignment:

Return to GapStreeze Input Page.




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