Find most similar peptide and calculate distance?
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2.5 years ago
wormball ▴ 10


I have mutant and wild peptide. I select some short subpeptide containing mutation and i want to find the most similar subpeptide (preferably of the same length) in the wild peptide to compare its immunological properties to the mutant one. And also i want to know some distance between them (e. g. Levenshtein distance). E. g. if distance is 0, then there is no need to consider this subpeptide at all, and if distance is larger than e. g. 2, then we say there is no similar wild subpeptide.

Is there a standard way to do so? I found pairwise2.align.globalxx in biopython, but it returns alignment score instead of distance and also returns alignments not in the most convenient way.

Thanks in advance.

align distance sequence peptide • 489 views

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