[Bioperl-l] from transcript to genes

zhang zhang lavende_dresden at hotmail.com
Wed Mar 28 05:50:24 EDT 2007


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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