[ensembl-dev] download gene structure

[Jan-hinnerk Vogel]

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
>
>
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
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