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

[Mark A. Jensen]

Excellent, Emanuele-- would you post your fix to the list?
thanks--MAJ
  ----- 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


  Hello everyone.
  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.
  Bye
  Emanuele

  P.S.
  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
    http://www.bioperl.org/wiki/Human_genomic_coordinates_and_sequence
    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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