Ehm.. I'm not a biologist, I only know someone... so you almost lost me there.

The BLAST and related algorithms do exactly what you asked for: they find all the possible matches between two sequences, ranking them by 'edit distance', i.e. the number of operations needed to obtain a perfect match.

This is really all I know, for details ask an expert ;-)

-- 
        dakkar - Mobilis in mobile

Most of my code is tested...

Perl is strongly typed, it just has very few types (Dan)

In reply to Re^3: similar string matching by dakkar
in thread similar string matching by Anonymous Monk

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