[Bioperl-l] from transcript to genes

Chris Fields cjfields at uiuc.edu
Wed Mar 28 11:09:05 EDT 2007


As both Albert and Sendu point out, this is best asked on the ensembl- 
dev mail list.

In relation (and due) to this question I have added a few Ensembl- 
related questions to the FAQ.  If anyone has corrections on those  
please feel free to make them.

chris

On Mar 28, 2007, at 4:50 AM, zhang zhang wrote:

> Thanks Albert,
>
> But now if I have a string of transcripts like  
> ('ENSDART00000011751','ENSDART00000002250' and more). I want to  
> find their corresponding genes how to do it?
>
> I have tried:
> $transcript_adaptor->fetch_by_stable_id 
> ("ENSDART00000011751",'ENSDART00000002250');
>
>
> doesnot work! except using the loop, any easy idea?
>
> Cheers Yanju
>
>
>> From: "Albert Vilella" <avilella at gmail.com>
>> To: "zhang zhang" <lavende_dresden at hotmail.com>, bioperl-l
> <Bioperl-l at lists.open-bio.org>
>> Subject: Re: [Bioperl-l] from transcript to genes
>> Date: Wed, 28 Mar 2007 10:41:14 +0100
>>
>> Hi Zhang,
>>
>> This question is more for the ensembl-dev mailing list:
>> ensembl-dev at ebi.ac.uk than the bioperl ml.
>>
>> You can get the gene object from the transcript object with a  
>> script like
>> this:
>>
>> ----
>>
>> use strict;
>> use Bio::EnsEMBL::Registry;
>>
>> Bio::EnsEMBL::Registry->load_registry_from_db(- 
>> host=>"ensembldb.ensembl.org",
>
>> -user=>"anonymous", -verbose=>'0');
>>
>> my $transcript_adaptor = Bio::EnsEMBL::Registry->get_adaptor 
>> ("Danio rerio",
>> "core", "Transcript");
>> my $transcript =
>> $transcript_adaptor->fetch_by_stable_id("ENSDART00000011751");
>>
>> my $gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Danio rerio",
>> "core", "Gene");
>> my $gene_from_transcript =
>> $gene_adaptor->fetch_by_transcript_id($transcript->dbID);
>>
>> print "transcript_stable_id: ", $transcript->stable_id, "\n";
>> print "gene_stable_id: ", $gene_from_transcript->stable_id, "\n";
>> print "Chromosome: ",  $gene_from_transcript->seq_region_name, "\n";
>> print "Strand (1,-1): ",  $gene_from_transcript- 
>> >seq_region_strand, "\n";
>> print "Start: ", $gene_from_transcript->seq_region_start, "\n";
>> print "End: ", $gene_from_transcript->seq_region_end, "\n";
>>
>> 1;
>>
>> ----
>>
>> Cheers,
>>
>>    Albert.
>>
>>
>> On 3/28/07, zhang zhang <lavende_dresden at hotmail.com> wrote:
>>>
>>> Dear all,
>>>
>>> I just begin to use Ensembl perl API. for example, now I have  
>>> zebrafish
>>> transcrits like "ENSDART00000011751", how can I find its  
>>> corresponding
>>> gene
>>> and further get gene's location such chromosome, start, end  
>>> information?
>>>
>>> what kinds of ensembl database and adaptors or methods should I use?
>>>
>>> Thanks,
>>> Yanju Zhang
>>>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






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