[BioC] Get gene structure information: use biomaRt or other annotation packages?

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Sat Mar 20 21:37:51 CET 2010

Something like this?


mart.obj <- useMart(biomart = 'ensembl', dataset = 'hsapiens_gene_ensembl')

atb <- c('ensembl_gene_id', 'ensembl_transcript_id','5_utr_start',

locs <- getBM(attributes=atb, mart=mart.obj)

I haven't tested it yet....
From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Zhu, Julie [Julie.Zhu at umassmed.edu]
Sent: 20 March 2010 19:33
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Get gene structure information: use biomaRt or other annotation packages?


I need to get the following information in one file and thinking of using
getBM method in biomaRt to get each feature type separately and then combine
them in one file. I am wondering if there is a more elegant way to do this
in biomaRt or does there exist an annotation package that contains the
following information for different species?

EnsembleGeneID  Chromosome FeatureStart  FeatureEnd  Strand  FeatureType

The feature types I am interested in are 5' UTR, 3' UTR and Exon.

Thank you very much for your kind help!

Best regards,


Lihua Julie Zhu, Ph.D
Research Associate Professor
Program in Gene Function and Expression
University of Massachusetts Medical School
364 Plantation Street, Room 613
Worcester, MA 01605

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