[Bioperl-l] Getting genomic coordinates for a list of genes
Mark A. Jensen
maj at fortinbras.us
Thu Jul 23 19:33:42 EDT 2009
Excellent, Emanuele-- would you post your fix to the list?
----- Original Message -----
From: Emanuele Osimo
To: Mark A. Jensen
Cc: perl bioperl ml
Sent: Thursday, July 23, 2009 7:24 PM
Subject: Re: [Bioperl-l] Getting genomic coordinates for a list of genes
Today I discovered that the coupling of the two subs that Mark posted doesn't get the right results. I think this is because one gets the coordinates with RefSeq build 36.3, the other with build 37.
I found that coupling the first sub, genome_coords, with the Bio::EnsEMBL::Registry fetch by region API is a lot better, and it actually generates sequences that contain the genes.
Thanks a lot to Mark!!
On Thu, Jul 23, 2009 at 16:16, Mark A. Jensen <maj at fortinbras.us> wrote:
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
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
More information about the Bioperl-l