[Bioperl-l] Re: Given a protein sequence (and its Genbank accession number)

[Barry Moore]

Wuming-

Try the file gene2refseq and/or gene2accession from 
ftp://ftp.ncbi.nih.gov/gene for the mapping.  It lists mRNA and protein 
ids.  After you've got you mRNA ids, use  Bio::DB::RefSeq to grab the 
mRNA, and extract the CDS coordinates from the features table as you 
suggested, and then the sequence.

B

Wuming Gong wrote:

>Hi list, 
>
>In fact, I wanna get the coding sequences of the given proteins. Can I
>perform the job by tblastn the proteins to refseq databases followed
>by extracting the CDS sequences according to the start and end locus
>of CDS in the SeqFeature section ? Thanks.
>
>Wuming
>
>
>On Fri, 3 Dec 2004 18:48:23 +0800, Wuming Gong <gongwuming at gmail.com> wrote:
>  
>
>>Hi list,
>>
>>Could you please give me some clues on how to map a protein sequences
>>which accession number is already known to a mRNA sequences in
>>GenBank?
>>
>>Thanks!
>>
>>Wuming
>>
>>    
>>
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>

-- 
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT


-- 
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT