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 Gap Strip

Goal: You want to remove all columns from your alignment that contain one or more gaps. This is called gap stripping.

Data: The alignment in the box below contains a single gap in column 2, and all gaps in column 4.

Settings:
1. The tolerance for gaps has been set to zero, so both these columns will be removed ("stripped") when you press the Run button and leave the 'Preserve codons' checkbox unchecked.
2. If 'Preserve codons' is checked and you set both, the number of tolerance positions and the reading frame to 1 then the first two codons will be stripped.
3. If 'Preserve codons' is checked and you set the number of tolerance positions to 1 but change the reading frame to 2, then the first codon (starting at position 2) is stripped.

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 Gap Strip/Squeeze Input Page.




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