[Bioperl-l] matrix from bl2seq

Giovanni Coppola gcoppola at ucla.edu
Fri Jan 6 12:58:24 EST 2006

Hi Wyatt,
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!
Thanks again

On Jan 6, 2006, at 9:13 AM, kevin.mcmahon at ttuhsc.edu wrote:

> Giovanni,
> 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  
> frac_identical
> 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
> <http://bioperl.org/HOWTOs/html/SearchIO.html> .  It sure helped me!
> Good luck,
> Wyatt
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