[BiO BB] Re: Quickly retrieving cross-referenced records from NCBI

J.W. Bizzaro jeff at bioinformatics.org
Wed Dec 20 17:18:26 EST 2006

Stan, the attached script got removed.  Please resend it in-line (in the message body), or send a link.  Thanks, Jeff

Gaj Stan (BIGCAT) wrote:
> Dear Dale,
> I encountered the same question a few weeks ago, but my focus was the
> other way around: go from NM to NP. For that I've written a Perl script
> that I've adjusted to fit your needs (so going for NP to NM).
> If I'm correct, RefSeq splits it's database in three parts: genomic,
> mRNA and protein. For this script to work, you need a) to download a
> species-specific RefSeq mRNA database (ends with .rna.gbff) for the NCBI
> ftp and b) to have your own file of convertable IDs, sorted in a
> list-form..
> Note that this script will NOT detect version numbers: e.g. XP_12345.1
> needs to be converted to XP_12345 in your list before it does it's job!
> Although the code is far from perfect, it fulfills your question
> perfectly (-;
> Best wishes,
>    Stan

J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 508 890 8600

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