[BioPython] NCBI: from protein to CDS
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"
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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