[Bioperl-l] divide and blast blastunsplit blast subsequence

[Chris Fields]

There is a script that comes with the bioperl core distribution,  
bp_split_seq.pl, which does this.  Here's the CVS location:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/ 
scripts/seq/?cvsroot=bioperl

chris

On Oct 2, 2007, at 1:21 AM, Kevin Lam wrote:

> Hi!
> I am trying to annotate a 200kb sequence by doing blastx to find  
> the protein
> seq location
> I need to split the sequence up so that I get the best hits for  
> each region
> (the top blast hits will mask the smaller proteins if i do it as a  
> whole
> sequence)
> if i were to do it manually i can set the subsequence in the web  
> gui for
> ncbi's blast.
> this way, the blast hits coords are based on the whole 200kb.
>
> but I can't find this option in blast or a straightforward way to  
> do it in
> bioperl.
>
> I found similar solutions like
> http://www.bio.davidson.edu/projects/DAB/DAB.html
> divide and blast (but I need to specify coords)
>
> there also this from the bioperl archives
> http://bioinformatics.org/pipermail/bioclusters/2002-August/ 
> 000375.html
>
> but isn't there an easier way like i can specify blast subsequence  
> 200-900
> of fasta file and it will return the blastx hits in coords in terms  
> of the
> whole 200kb?
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign