[Bioperl-l] **Fwd: Re: divide and blast blastunsplit blast subsequence

Chris Fields cjfields at uiuc.edu
Thu Oct 11 09:49:59 EDT 2007

Yep, started using this myself for mapping old predicted CDS onto new  
assemblies using BLASTX.  Works very well, particularly since it  
retains the seq position on hits, where using bp_slit_seq would  
require mapping to the correct coordinates.


On Oct 11, 2007, at 6:32 AM, Kevin Lam wrote:

> wow thanks for the replies!
> I have gotten the answer from the blast help
> Subsequence range can be specified by the –L parameter. Please refer
> to this web document for more information:
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/ 
> blastall_node60.html
> Other end-user oriented standalone blast documents are at:
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/
> but will try this method as well to see which works better.
> cheers!
> kevin
> 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
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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