I was thinking of using substr initially, but was having difficulty with the presence of gaps in the alignment throwing off the numbering. Thus I was going through the string counting non-gap characters, and figured it would be faster and easier to read in the strings and generate a lookup hash.

The expected output for T281 would be a gap without a position number, or just return false. Based on how the alignments are done, it would be highly unlikely for a desired residue in the query strand to align with a gap in the subject strand. Likewise, K280 would return Q137, and I282 would return F138.

In reply to Re: Per residue sequence alignment - per character string comparison? by proteins
in thread Per residue sequence alignment - per character string comparison? by proteins

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