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Highlighter for Nucleotide Sequences v2.2.3

Purpose: This tool highlights matches, mismatches, transition and transversion mutations, and silent and non-silent mutations. The nucleotide sequences must be aligned and in frame. This tool 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

Or upload sequence file
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
Transitions and Transversions
Silent and Non-silent Mutations
Matches
Sort sequences by similarity by tree Do not sort
Treat gaps as character? Yes No
Handling IUPAC codes Ignore Use codes to match Treat codes as characters

Options for Highlighting Mismatches
The following options apply only if you chose "Mismatches" above:
Mark APOBEC signatures

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

last modified: Tue Jan 7 12:49 2014


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

 
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