Re: similar string matching

The algorithms are quite well established, but they're not obvious. If you try to roll your own, you'll quite probably end up with very slow matching. Look at http://www.bioperl.org/ and you'll find all the information you need.

The short version: use BLAST or derived methods.

-- 
        dakkar - Mobilis in mobile

Most of my code is tested...

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

Comment on Re: similar string matching

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Re^2: similar string matching by Anonymous Monk on Jul 05, 2004 at 19:22 UTC
Nice hint but what if I want to find single amino acid sequences? like cystine bridges? Murcia	[reply]
Re^3: similar string matching by dakkar (Hermit) on Jul 05, 2004 at 19:41 UTC
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)	[reply]