Hi Michael, Thank you very much for the code snippet! Best regards,, Julie On 3/20/10 4:39 PM, "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk> wrote: library(biomaRt) mart.obj <- useMart(biomart = 'ensembl', dataset = 'hsapiens_gene_ensembl') atb <- c('ensembl_gene_id', 'ensembl_transcript_id','5_utr_start', '5_utr_end','3_utr_start','3_utr_end','ensembl_exon_id ','exon_chrom_start', 'exon_chrom_end','rank','phase') locs <- getBM(attributes=atb, mart=mart.obj) ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Zhu, Julie [Julie.Zhu@umassmed.edu] Sent: 20 March 2010 19:33 To: bioconductor@stat.math.ethz.ch Subject: [BioC] Get gene structure information: use biomaRt or other annotation packages? Hi, 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 FeatureID The feature types I am interested in are 5' UTR, 3' UTR and Exon. Thank you very much for your kind help! Best regards, Julie ******************************************* 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 508-856-5256 http://www.umassmed.edu/pgfe/faculty/zhu.cfm _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]