[ensembl-dev] download gene structure

[Maximilian Haussler]

Hi Liu,

you can look onto the code of the evidence view in Ensemb, e.g.
http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000139618;r=13:32889611-32973347;t=ENST00000380152

You can probably re-use a lot of the perl code that is used to
generate this page...

cheers
Max



On Tue, Dec 7, 2010 at 10:16 AM, Jan-hinnerk Vogel <jhv at sanger.ac.uk> wrote:
> Hi Liu,
>
> one way to do this would be to use the ensembl API - if you're familiar with
> perl . We provide supporting features for transcripts
> and exons - you can call methods on the Exon and Transcript objects to
> retrieve them. This support is added to transcripts / exons
> during the 'gene build' process.
>
> Another way to do this would be to cluster the exons of the genes you're
> interested in together with the
> exons of the support (ie cDNAs) and calculate a score yourself - for example
> to calculate how many times an Exon overlaps a cDNA.
> The gene data can be found in the core databases and the cDNA data is
> usually in the _otherfeature_ (or _cdna_ ) databases.
>
> There are some routines in  some routines in the ensembl-analysis cvs
> checkout which you can use for the clustering.
> The ClusterUtils.pm exports some methods for this, too.
>
> ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Tools/Algorithms/ExonCluster.pm
> ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Tools/Algorithms/GeneCluster.pm
> ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Tools/Algorithms/IntronCluster.pm
> ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Tools/Algorithms/TranscriptCluster.pm
> ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Tools/Algorithms/ClusterUtils.pm
>
>
> Hth,
>                Jan Vogel
>
>
>
>
> --
> Ensembl Genebuild Team Project Leader
> www.ensembl.org
>
>
>
> On 6 Dec 2010, at 22:10, Liu,Bin wrote:
>
>> Hi,
>>        I was trying to retrieve the gene structures for serveral species.
>> I wonder if there is a way to retrieve the information that support the
>> model of each genes. I realized that Flybase provides those information for
>> genes on Drosophila genome. For example, there are tracks in Flybase that
>> indicate how strong (a score) of the evidence supporting the current gene
>> model and what the evidance are (est, cDNA or others).
>>        Thanks for your help.
>>
>>
>> Bin Liu, Ph.D.
>> Department of Genetics
>> The University of Texas M. D. Anderson Cancer Center
>> 1515 Holcombe Blvd
>> Houston, TX 77030
>> Phone:  713-792-0878
>> Email: bliu1 at mdanderson.org
>> Room No: S13.8316A
>>
>>
>>
>> _______________________________________________
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>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
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