How I Wrote an Ultra-Fast DNA Sequence Alignment Algorithm in JavaScript

Re:How I Wrote an Ultra-Fast DNA Sequence Alignment Algorith... by iten on Monday February 23, 2015 @02:01PM (#9096204)

What proportion of bases in your query were ambiguous? If it was a fairly low percentage (~10-20%?), I think you could probably get away with using LASTZ, treating all ambiguous bases as completely ambiguous (--ambiguous=iupac), then write a short script to go through the alignments afterward and filter out ones that don't have a reference base that matches the IUPAC character in the query.

But that's the lazy approach :) Good article.

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Re:How I Wrote an Ultra-Fast DNA Sequence Alignment Algorith... by keithwhor on Monday February 23, 2015 @02:52PM (#9096551)

Thanks. :)

Sometimes reinventing a wheel (or at the very least a spoke or two) can be fun and provide some neat results.

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