[BioPython] NCBI: from protein to CDS

Iddo Friedberg idoerg at burnham.org
Thu Apr 10 18:02:50 EDT 2003


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 :


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 

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...



Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171

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