[Bioperl-l] Getting genomic coordinates for a list of genes
Mark A. Jensen
maj at fortinbras.us
Thu Jul 23 19:16:18 EDT 2009
Sorry, went off-list for a couple cycles. The final product will get the
correct chromosomal coordinates and then return the sequence from
the current build, based on a geneID input. See
for the results.
----- Original Message -----
From: "Emanuele Osimo" <e.osimo at gmail.com>
To: "perl bioperl ml" <bioperl-l at lists.open-bio.org>
Sent: Friday, July 17, 2009 8:49 AM
Subject: [Bioperl-l] Getting genomic coordinates for a list of genes
> Hello everyone,
> I'm new to programming, I'm a biologist, so please forgive my ignorance, but
> I've been trying this for 2 weeks, now I have to ask you.
> I'm trying the script I found at
> because I need to have some variables (like $from and $to) assigned to the
> start and end of a gene.
> The script works fine, but gives me the wrong coordinates: for example if I
> try it with the gene 842 (CASP9), it prints:
> NT_004610.19 2498878 2530877
> I found out that in Entrez, for each gene (for CASP9, for example, at
> ) under "Genome Reference Consortium Human Build 37 (GRCh37),
> Primary_Assembly" there are two different sets of coordinates. The first is
> called "NC_000001.10 Genome Reference Consortium Human Build 37 (GRCh37),
> Primary_Assembly", and is the one I need, and the second one is called just
> "NT_004610.19" and it's the one that the script prints.
> This is valid for all the genes I tried.
> DO you know how to make the script print the "right" coordinates (at least,
> the one I need)?
> Thanks a lot in advance,
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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