[Bioperl-l] Getting genomic coordinates for a list of genes

Mark A. Jensen maj at fortinbras.us
Thu Jul 23 23:16:18 UTC 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.
cheers MAJ
----- 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
> http://bio.perl.org/wiki/HOWTO:Getting_Genomic_Sequences#Using_Bio::DB::EntrezGene_to_get_genomic_coordinates
> 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
> http://www.ncbi.nlm.nih.gov/gene/842?ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum#refseq
> ) 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,
> Emanuele
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