[BioC] Obtaining exon structure of a gene via Bioconductor

[Michael Dondrup]

Hi,
this is also possible with biomart and therefore also with biomaRt.
The following query gives an example. Fetches all exon sequences for  
C. elegans Gene with ensembl-geneid T24D1.1 in fasta format.
(try this url)

http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=celegans_gene_ensembl.default.sequences.ensembl_gene_id|celegans_gene_ensembl.default.sequences.ensembl_transcript_id|celegans_gene_ensembl.default.sequences.gene_exon&FILTERS=celegans_gene_ensembl.default.filters.ensembl_gene_id."T24D1.1"|celegans_gene_ensembl.default.filters.biotype."protein_coding"&VISIBLEPANEL=resultspanel

If you like this, parameters can be almost directly translated into the the corresponding query in biomaRt although I don't think this is necessary for this case.

Best
Michael

Am Feb 2, 2010 um 5:08 PM schrieb Ruppert Valentino:

> 
> 
> 
> Hello,
> 
> 
> 
> I want to do heteroduplex on each exon of around 50 genes. Getting the exon structure for each gene from Ensembl and manually identifying the exon sequence seems very laborous.
> 
> 
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> Is there a way using Bioconductor package to get the exon sequences for all the transcripts of a gene, if so how can I do this, would biomaRt do it, if so how?
> 
> 
> 
> Anyway examples of a script or ideas is greatly appreciated as it takes hours to get all the exon sequences for a gene split up into files to use for PCR.
> 
> 
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> thanks in advance for any help on this.
> 
> 
> 
> Raphael
> 		 	   		  
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