Unless your sequence is quite large (and so you have many thousands of unique 20mers), I would go the hash route. It will be VERY fast if memory isn't limiting. If that isn't feasible, break your sequence into fasta sequences of size 20 base pairs and give each a unique ID. Then, blast away using tabular output. Then, you can parse to your heart's content using simple perl.

Sean

In reply to Re^3: Parsing BLAST by srdst13
in thread Parsing BLAST by cumurph

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