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

[Smithies, Russell]

It's still available on the new site but only as an old version - v2.0a19 (but it's now free)
http://www.advbiocomp.com/blast/obsolete/


--Russell

> -----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
> WUBlast
> 
> Hello,
> this is the fix:
> 
> use Bio::EnsEMBL::Slice;
> use Bio::EnsEMBL::Registry;
> 
> my $db = new Bio::DB::EntrezGene;
> 
> my $registry = 'Bio::EnsEMBL::Registry';
> $registry->load_registry_from_db(
>    -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?
> 
> Thanks
> Emanuele
> 
> 
> 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
> >>>
> >>>
> http://bio.perl.org/wiki/HOWTO:Getting_Genomic_Sequences#Using_Bio::DB::Entrez
> Gene_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
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>
> >
> >
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================