[Bioperl-l] bioperl dna pairwise local alignment

[Mike Pheasant]

Hi,

I need to do lots of pairwise local alignments on short DNA sequences (up to
100 nt). I was hoping to use the pSW module but this only works for protein,
and the other options with standaloneblast and clustalw require system calls
to execute the binaries, and I'd rather avoid the overhead for the number of
aligns I want to do.

Has anyone linked the water.c code from EMBOSS into perl ?
Are there any other perl modules anyone knows about which do this?

Alternatively has anyone linked local alignment code into an SQL function in
MySQL or PostgresQL ?
My sequence data is in a database, and I could do it that way as well.

Thanks,

Mike Pheasant.