[Biopython] Dealing with Non-RefSeq IDs / InParanoid

Matthew Strand stran104 at chapman.edu
Wed Jul 1 06:18:42 EDT 2009

Sure, I can create a page tomorrow when I get into the office. Perhaps
"Retrieving Sequences Based on ID" would be appropriate. Alternative
suggestions are welcome.

On Tue, Jun 30, 2009 at 8:53 PM, Iddo Friedberg <idoerg at gmail.com> wrote:

> Thanks. There is a wiki-based cookbook in the biopython site. Would you
> like to put it up there?
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
> On Jun 30, 2009 8:02 PM, "Matthew Strand" <stran104 at chapman.edu> wrote:
> For the benefit of future users who find this thread through a search, I
> would like to share how to retreive a sequence from NCBI given a non-NCBI
> protein ID (or other ID). This was question 3 in my original message.
> Suppose you have a non-NCBI protein ID, say CE23997 (from WormBase) and you
> want to retrieve the sequence from NCBI.
> You can use Bio.Entrez.esearch(db='protein', term='CE23997') to get a list
> of NCBI GIs that refrence this identifer. In this case there is only one
> (17554770).
> Then you can get the sequence using Entrez.efetch(db="protein",
> id='17554770', rettype="fasta").
> This may be obvious to some, but it was not to me; primarially because I
> was
> unaware of the esearch functionality.
> --
> Matthew Strand
> _______________________________________________ Biopython mailing list -
> Biopython at lists.open-bio....

Matthew Strand

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