[Bioperl-l] Getting genomic coordinates for a list of genes AND WUBlast
Russell.Smithies at agresearch.co.nz
Thu Jul 23 22:31:06 EDT 2009
It's still available on the new site but only as an old version - v2.0a19 (but it's now free)
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Emanuele Osimo
> Sent: Friday, 24 July 2009 12:48 p.m.
> To: Mark A. Jensen
> Cc: perl bioperl ml
> Subject: Re: [Bioperl-l] Getting genomic coordinates for a list of genes AND
> this is the fix:
> use Bio::EnsEMBL::Slice;
> use Bio::EnsEMBL::Registry;
> my $db = new Bio::DB::EntrezGene;
> my $registry = 'Bio::EnsEMBL::Registry';
> -host => 'ensembldb.ensembl.org',
> -user => 'anonymous'
> my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' );
> my $slice = $slice_adaptor->fetch_by_region( 'chromosome', $chr, $start, $end
> print $slice->seq ;
> To be used after getting the coordinates with sub genome_coords .
> I have another question for you: I need to use the software WUBlast,
> but I noticed that it is no more available on the website. They just
> say that if you have it, you can use it. I don't have it, but I
> urgently need it, if anyone has it, could you please send it to me?
> On Thu, Jul 23, 2009 at 16:33, Mark A. Jensen<maj at fortinbras.us> wrote:
> > 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
> >>> 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,
> >>> Emanuele
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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