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HIV sequence database



Highlighter

Purpose: This tool highlights matches, mismatches, transition and transversion mutations, and silent and non-silent mutations in a set of nucleotide sequences that are aligned and in frame. It is particularly useful for allowing visualization of 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 if aligning against a single master. In case of multiple master sequences (during match), the top n will be chosen as master sequences. For descriptions of options and samples of output, see Highlighter Explanation.

Input
Paste your alignment

Or upload sequence file
Click to change masters

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 Jul 27 15:11 2010


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

 
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