[BioPython] NCBI: from protein to CDS
Iddo Friedberg
idoerg at burnham.org
Thu Apr 10 19:24:29 EDT 2003
Sorry, slight mistake in my question.
The protein sequence is retrieved using the gi-10956263
Then the CDS link hold the following:
val=10956247 (which is the nucleotide GI)
itemID=98 (which tells us which bit of the nucleotide sequence actually
codes for this protein).
Best,
Iddo
Iddo Friedberg wrote:
> Hi,
>
> Can anyone suggest a painless way to retrieve a coding sequence using a
> protein gi number via NCBI? manually that would mean to:
>
> 1) go to the protein page using the protein gi.
> 2) Click on the CDS
> 3) Get the DNA sequence coding to it.
>
> Here why this is a bummer:
>
> Using the gi-10956247 a protein record is retrieved from NCBI. The URL
> for the CDS looks like :
>
> "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=10956247&itemID=98&view=gbwithparts"
>
>
> the "val" field holds the same gi number, but the itemID field varies
> (that depends on the coding location in the full genome record, in this
> case). So I cannot use the protein gi to go and retrieve its coding
> sequence.
>
> I *can* write something to read the URL itemID field value, I just
> thought there might be a more elegant way. Maybe even using "legitimate"
> NCBI mechanisms...
>
> Thanks,
>
> Iddo
>
>
>
--
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://bioinformatics.ljcrf.edu/~iddo
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