Question: Obtaining promoter sequences with biomaRt R package
gravatar for ilyco
5.4 years ago by
United Kingdom
ilyco50 wrote:


I tried to obtain the promoter sequences of 22 genes (2000 bp upstream) using the biomaRt R package and their Ensembl Gene Ids. However, the getBM() function returns 'Sequence Unavailable' for 20 of the genes and only retrieves the sequences for 2 of the genes. Do you know why this is happening and what alternatives do I have for obtaining the sequences?

I am using an archived version of the Ensembl mart for mm9 mouse genome and the following code:

promoters <- getSequence(id = gene.names, type='ensembl_gene_id',seqType='coding_gene_flank',

where gene.names is a list of ensembl gene ids.

Thank you very much in advance!


promoter sequence biomart • 3.2k views
ADD COMMENTlink written 5.4 years ago by ilyco50

Is this true when you use biomart web instead biomaRt ?

ADD REPLYlink written 5.4 years ago by poisonAlien2.8k

Thank you!

I downloaded all the upstream sequences of all the genes from biomaRt and selected the genes I wanted afterwards using the Ensembl Ids.


ADD REPLYlink written 5.4 years ago by ilyco50
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1233 users visited in the last hour