
Thanks Michael
 
This looks great. I wonder if you could direct me to a page that explains the database schema that ensembl uses as I am interested in human genes and not sure what to put in the query to get say human TP53 gene exonic sequences?
 
thanks


 
> Subject: Re: [BioC] Obtaining exon structure of a gene via Bioconductor
> From: Michael.Dondrup@uni.no
> Date: Tue, 2 Feb 2010 17:41:39 +0100
> CC: bioconductor@stat.math.ethz.ch
> To: ruppert7@hotmail.com
> 
> 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.
> > 
> > 
> > 
> > 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.
> > 
> > 
> > 
> > thanks in advance for any help on this.
> > 
> > 
> > 
> > Raphael
> > 
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