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 Squeeze

Goal: You want to remove only those columns from your alignment that are entirely gaps. This is called gap squeezing.

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 100, so only column 4 will be removed ("squeezed") when you press the Run button.
2. If 'Preserve codons' is checked and you set both, the number of tolerance positions and the reading frame to 1 then the second codon will be removed.
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) will be removed.

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