[Bioperl-l] full chromosome accesscion number mess

[Guojun Yang]

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