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

[Chris Fields]

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.

chris

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