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

Thu Jul 23 23:20:09 EDT 2009

Himself, I believe-
some previous discussion at 
http://lists.open-bio.org/pipermail/bioperl-l/2009-May/030075.html

----- Original Message ----- 
From: "Smithies, Russell" <Russell.Smithies at agresearch.co.nz>
To: "'Chris Fields'" <cjfields at illinois.edu>
Cc: "'Emanuele Osimo'" <e.osimo at gmail.com>; "'Mark Jensen'" <maj at fortinbras.us>; 
"'BioPerl List'" <bioperl-l at lists.open-bio.org>
Sent: Thursday, July 23, 2009 11:15 PM
Subject: RE: [Bioperl-l] Getting genomic coordinates for a list of genes 
ANDWUBlast

Who's behind AdvBioComp?
I saw Warren Gish's name on a copyright notice at the bottom of one of their 
pages but I'm not sure if it's just a left-over WU-Blast page.

--Russell

> -----Original Message-----
> From: Chris Fields [mailto:cjfields at illinois.edu]
> Sent: Friday, 24 July 2009 3:05 p.m.
> To: Smithies, Russell
> Cc: Emanuele Osimo; Mark Jensen; BioPerl List
> Subject: Re: [Bioperl-l] Getting genomic coordinates for a list of genes AND
> WUBlast
>
> Unfortunately most users are bound by the previous licensing terms, b/
> c I know a few squirrels who have this lying around.  I think the
> newer version will be free for academic use if it ever makes the light
> of day.
>
> chris
>
> On Jul 23, 2009, at 9:31 PM, Smithies, Russell wrote:
>
> > 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
> >>>>>
> >>>>>
> >>>>
> >>>
> >>>
> >>
> >> _______________________________________________
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> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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