[Bioperl-l] matrix from bl2seq
gcoppola at ucla.edu
Fri Jan 6 12:58:24 EST 2006
thanks for your suggestion.
I was considering ClustalW and LALIGN and SSEARCH from FASTA as well,
since I am looking for perfect local alignments (I am designing
microarray probes and I am checking for homology regions of 25 bp).
I will end up trying several of them and choosing based on the
output.... anyway, it is a good exercise!
On Jan 6, 2006, at 9:13 AM, kevin.mcmahon at ttuhsc.edu wrote:
> I am new to Bioperl myself, so take my advice with a grain of
> salt. But, it
> sounds like you've got the right idea. If you're looking to make
> one of
> those charts that shows the percent identity between two sequences
> for every
> permutation, I'd do exactly what you're doing. And use the
> or frac_conserved (depending on what you want) methods from the
> Bio::Search::Hit module. For real information on how to do this,
> check out
> Jason Stajich's excellent review on the Bio::SearchIO module here:
> <http://bioperl.org/HOWTOs/html/SearchIO.html> . It sure helped me!
> Good luck,
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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