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

[Chris Fields]

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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