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.


Highlighter for Amino Acids v1.3.4

Purpose: This tool highlights matches and mismatches in a set of aligned amino acid sequences. It is particularly useful for visualizing potential recombination and hypermutation in closely related sequences, such as those isolated from a single patient.

Details: If the "Change Masters" button is not clicked, the first sequence in the file will be taken as the master sequence. In the case of multiple master sequences, the top n will be used. For descriptions of options and output, see Highlighter Explanation.

Input
Paste your alignment

[Sample Input]
Or upload sequence file
Ignore alphabet validation
Click to change masters Note: "Match" is the only case in which more than one master can be applied.

Options
Choose what to highlight Mismatches
Matches
Sort sequences by similarity by tree Do not sort
Treat gaps as character? Yes No

Options for Coloring Matches/Mismatches
Color matched/mismatched amino acids by selecting one of the following color schemes:
Standard Se-Al (default) Se-Al (polar/non-polar) BioEdit

Options for Highlighting Matches
The following options apply only if you chose "Matches" above:
Number of masters
Use bars to indicate successive matches? Yes No




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