I have a set of protein sequences (from Biomart ENSEMBL Release 62) of Homo sapiens. On these sequences I have run PFAM-HMMER to find domains on these sequences. I also have coordinates (coding sequence as well as genomic)for the exons that make up these proteins. I want to map the protein domains to these exons. How do I accomplish this in R and Bioconductor? Thanks in advance for any suggestions. Regards, Anupam [[alternative HTML version deleted]]

On Tue, Jan 3, 2012 at 12:49 PM, anupam sinha <anupam.contact@gmail.com>wrote: > I have a set of protein sequences (from Biomart ENSEMBL Release 62) of Homo > sapiens. On these sequences I have run PFAM-HMMER to find domains on these > sequences. I also have coordinates (coding sequence as well as genomic)for > the exons that make up these proteins. I want to map the protein domains to > these exons. How do I accomplish this in R and Bioconductor? Thanks in > advance for any suggestions. > > If you have genomic coordinates, you could use the GenomicRanges and GenomicFeatures Bioconductor packages to find overlaps between your PFAM regions and known exons. Sean [[alternative HTML version deleted]]