[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:

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 
>use strict;
>use Bio::EnsEMBL::Registry;

>-user=>"anonymous", -verbose=>'0');
>my $transcript_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Danio 
>"core", "Transcript");
>my $transcript =
>my $gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Danio 
>"core", "Gene");
>my $gene_from_transcript =
>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, 
>print "Start: ", $gene_from_transcript->seq_region_start, "\n";
>print "End: ", $gene_from_transcript->seq_region_end, "\n";
>    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 
>>transcrits like "ENSDART00000011751", how can I find its 
>>and further get gene's location such chromosome, start, end 
>>what kinds of ensembl database and adaptors or methods should I 
>>Yanju Zhang
>>ÓëÁª»úµÄÅóÓѽøÐн»Á÷£¬ÇëʹÓà MSN Messenger:  
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