[Bioperl-l] How to obtain the chromosome from an Accession Number

Sean Davis sdavis2 at mail.nih.gov
Wed Apr 13 21:07:23 EDT 2005


What kind of accession?  GenBank?  If so, then you can use the UCSC 
genome table browser (http://genome.ucsc.edu/cgi-bin/hgTables) to 
upload your list of all accessions and look them up in their mapping 
tables (mRNA and EST and knownGene).  You would need to upload your 
whole list to each of the possible organisms and then compile the final 
list from the species-specific lists.  Of course, these tables are all 
available as tab-delimited text for download from UCSC, so you could 
grab whichever you like and do it on your own machine.  Note that some 
accessions will not map to any chromosome of any organism and some will 
map to many chromosomes/locations in the organism from which they came.


On Apr 13, 2005, at 2:43 PM, Ryan Golhar wrote:

> Hi all,
> I have a bunch of accession numbers from different organisms, and I'm
> trying to determine the chromosome of their respective organism that
> they occur on.  Can I do this with BioPerl?
> Ryan
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