Dear All, Does anyone know that how to extract intragenic sequences from the genome. Like in the genescan, it is mentioned that the predictions are based on transcriptional, translational and donor/acceptor splicing signals as well as the length and compositional distributions of exons, introns and intergenic regions. But I am not sure which function I should use. Thank you very much. Yating Cheng Molecular Medicine Master's Program Charit?-Universit?tsmedizin Berlin

Hi, On Tue, Nov 29, 2011 at 6:25 AM, Yating Cheng <yating.cheng at="" charite.de=""> wrote: > Dear All, > > Does anyone know that how to extract intragenic sequences from the genome. > > Like in the genescan, it is mentioned that the predictions are based on > transcriptional, translational and donor/acceptor splicing signals as well > as the length and compositional distributions of exons, introns and > intergenic regions. > > But I am not sure which function I should use. Use the GenomicFeatures package to build a gene annotation database for your organism. By getting a bit more intimate with that package (good place to start is by reading its vignette, along with that for GenomicRanges) you will figure out how to identify where the intergenic regions lie on your genome. Once you have the intergenic regions of your genome stored in a GRanges object, its easy to use those ranges to get the sequence from your genome using the appropriate BSgenome.* package for your organism. The Biostrings::getSeq function could do that for you, among other things. HTH, -steve > > > Thank you very much. > > > > > Yating Cheng > Molecular Medicine Master's Program > Charit?-Universit?tsmedizin Berlin > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact