[Bioperl-l] Gene Id converts.

[Chris Fields]

There are the GenBank LiveLists (updated every Sunday), which has  
accession/version/UID mappings for nuc and protein GenBank records.  I  
haven't used it personally but it's worth a look:

ftp://ftp.ncbi.nih.gov/genbank/livelists/
There is also gene2accession, which contains mappings between  
accession and UID (though this is more EntrezGene-related, I believe):
ftp://ftp.ncbi.nih.gov/gene/DATA/

Both have documentation detailing formats.  I would recommend using  
one of the above two on a local database setup if you plan on  
converting a large number of accessions.

Bio::DB::EUtilities can also do this but is web-based via eutils.   
There are a couple of stub examples in the Cookbook HOWTO under  
'efetch' on converting accessions to UID (and vice versa), though note  
there is no one-to-one correspondence.  You can also convert UIDs to  
accessions using 'esummary' but the converse (accession to GI)  
requires, strangely, using efetch to grab the UIDs first, then re- 
retrieving the acccessions via esummary for one-to-one correspondence.
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook

chris

On Mar 29, 2008, at 11:09 AM, Jinyan Huang wrote:

> Hi,
>
> I have a list of gene bank accession id. I want to convert these ids  
> to NCBI id.
>
> For example:
>
>> From NM_011917 to 2919914.
>
> How can I do it?
>
> Thanks
>
>
> -- 
> Best regards,
> Jinyan Huang (ekeen)
> School of Life Sciences and Technology, 1302 Room
> Tongji University
> Siping Road 1239, Shanghai 200092
> P.R. China
> Tel :0086-21-65981041
> Msn: hiekeen at hotmail.com
> eMail: hiekeen at gmail.com
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign