[Bioperl-l] BLAST and parsing question

[Marc Logghe]

Hi Robert,
It should be possible to do it with blast also by fiddling with the
blast options. You could set the word size to 20 as you are not
interested in smaller hits for instance. Also, the hits are ranked so
you easily can check the best hit (taking first line of tabular blast
output) and check whether the hit length is 20 as well. Enlarging the
word size and producing tabular output will definitely increase the
speed.
My $0.02
Regards,
Marc 


  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Robert Murphy
> Sent: Monday, April 24, 2006 4:12 PM
> To: torsten.seemann at infotech.monash.edu.au
> Subject: Re: [Bioperl-l] BLAST and parsing question
> 
> Yes, that's basically it.  Find out which 20 unit long 
> subsequences of my sequence are not found in my database.
> 
> -Robert
> 
> 
> So you want all length 20 subsequences (derived using a 
> sliding window from some set of sequences) which are do not 
> appear in some other set of sequences (virus-db) ?
> 
> --
> Torsten Seemann <torsten.seemann at infotech.monash.edu.au>
> Victorian Bioinformatics Consortium
> 
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