[BioC] intron sequences from biomaRt

Durinck, Steffen (NIH/NCI) [F] durincks at mail.nih.gov
Fri Jun 15 15:32:24 CEST 2007

Dear Dario,

No there is currently no possibility to select intronic sequences directly.  You could request this at helpdesk at ensembl.org and see if they want to add this feature in future versions of Ensembl.  For now the only way to do it with biomaRt would be to retrieve the transcript or gene sequences and the exon sequences and then find the intronic sequences by splitting the transcript sequences on the different exons.  

Hope this helps,

-----Original Message-----
From: Dario Greco [mailto:dario.greco at helsinki.fi]
Sent: Fri 6/15/2007 9:13 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] intron sequences from biomaRt
dear list,

i need to get the intron sequences for a group of entrez gene ids.
is there any way to do it using biomaRt? apparently there is no option in the 
getSequence() function.

> sessionInfo()
R version 2.5.0 (2007-04-23)
 biomaRt    RCurl      XML
"1.10.0"  "0.8-1"  "1.7-3"

any suggestions?
thanks for your help.



Dario Greco

Institute of Biotechnology - University of Helsinki
Building Cultivator II
P.O.Box 56      Viikinkaari 4
FIN-00014       Finland

Office: +358 9 191 58951
Fax: +358 9 191 58952
Mobile: +358 44 023 5780

Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list