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

[Ryan Golhar]

I found a way to go it using Entrez Gene and the NCBI uetils tools.  It
returns the information in ASN.1 format.  I see from another thread a
parser for this is being worked on.  Thanks for your help,

-----
Ryan Golhar
Computational Biologist
The Informatics Institute at
The University of Medicine & Dentistry of NJ

Phone: 973-972-5034
Fax: 973-972-7412
Email: golharam at umdnj.edu

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Sean Davis
Sent: Tuesday, January 06, 1970 4:50 AM
To: Sean Davis
Cc: 'Bioperl List'
Subject: Re: [Bioperl-l] How to obtain the chromosome from an Accession
Number


And, I forgot to mention, I don't think there is a way to do this 
directly in bioperl, although perl is likely to be useful in this 
process.

Sean

On Jan 6, 1970, at 4:44 AM, Sean Davis wrote:

> Ryan,
>
> 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.
>
> Sean
>
> 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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