matrix from bl2seq

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

matrix from bl2seq

kevin.mcmahon
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
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://portal.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|

Re: matrix from bl2seq

Giovanni Coppola
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
Giovanni



On Jan 6, 2006, at 9:13 AM, [hidden email] 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
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://portal.open-bio.org/mailman/listinfo/bioperl-l