[BioC] biomaRt difference from biomart.org?

Jorrit Boekel jorrit.boekel at ki.se
Thu Dec 18 15:08:57 CET 2008

Dear list,

I have tried to fetch 1000bp upstream sequences for a number of rat 
genes via biomart. When using the webbased biomart this seems to work 
alright, but when automating the process I ran into a problem: for some 
genes, "Sequence unavailable" is returned.

Exemplifiyng for a single gene that has this problem:
 > sqmrtjb<-useMart("ensembl","rnorvegicus_gene_ensembl")
 > getSequence(id="ENSRNOG00000005152", 
type="ensembl_gene_id",seqType="coding_gene_flank", upstream=1000, 
                     V1                 V2
1 Sequence unavailable ENSRNOG00000005152

On the web, I select ("Attributes->Sequences->Flank(gene), upstream 
1000bp, and some associated gene data (Ensembl Gene id, assoc. gene name).

Am I unknowingly querying for different things? Or is the biomaRt 
interface connected to a different mart?


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