[Bioperl-l] full chromosome accesscion number mess

Chris Fields cjfields at uiuc.edu
Tue Feb 21 14:25:02 EST 2006


What is the accession you're having problems with?

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Guojun Yang
> Sent: Tuesday, February 21, 2006 12:46 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] full chromosome accesscion number mess
> 
> Hi, everybody,
> In the process of reparing my CGI script after NCBI blast output format
> change, I noticed that the accession number for rice pseudochromosome is
> very confusing and cause trouble for sequence retrieving. My script use
> remoteblast to search for similar sequences,and then retrieve the hit
> sequence with a bit flanking region from GenBank. The rice
> pseudochromosomes have accession numbers similar to that of the individual
> clones like AP00XXX. I do not want the sequence retrieving to involve
> these accessions because it takes forever. Can anybody give some
> suggestion on how to deal with it?
> Thanks,
> 
> 
> Guojun Yang
> Department of Plant Biology
> University of Georgia
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