dear BC folks: I gather most activities in the R/BC community are centered around RNA and the manipulation of expression data. However, in addition I am interested in control sequences in DNA and wonder if there are any tools (within R or another (similar?) environment) that would allow one to search large chunks of sequence for enrichment for any known cis-acting control elements (promoters, enhancers, silencers, repeat elements, MAR's, etc.)? I'm not sure if this is the appropriate list on which to inquire, but I'd much appreciate any feedback, or direction to another forum. with thanks, Jonathan

There are lots of such tools, both to search known databases or to search for self-described patterns. The following link shows lots of such ones. http://bip.weizmann.ac.il/bio_tools/dna-tools.html If you're going to search genomic sized chunks, a program I wrote called 'tacg' is pretty good and searches for IUPAC patterns (with or without errors), regular expressions, matrix descriptions, as well as for windows satisfying rules for the above: ((pattern A AND pattern B) NOT (Pattern C AND pattern D)) XOR (Pattern E NOT PAttern F)) in a sliding window of 1500 bases. for example. Described in more detail at: http://www.biomedcentral.com/1471-2105/3/8 Lemme know if you want the latest version. Runs on linux, MacOSX, Solaris, probably other *nixs hjm Johnnidis, Jonathan wrote: > dear BC folks: > > I gather most activities in the R/BC community are centered around RNA and the manipulation of expression data. However, in addition I am interested in control sequences in DNA and wonder if there are any tools (within R or another (similar?) environment) that would allow one to search large chunks of sequence for enrichment for any known cis-acting control elements (promoters, enhancers, silencers, repeat elements, MAR's, etc.)? > > I'm not sure if this is the appropriate list on which to inquire, but I'd much appreciate any feedback, or direction to another forum. > > with thanks, > > Jonathan > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- Cheers, Harry Harry J Mangalam - 949 856 2847 (vox; email for fax) - hjm@tacgi.com <<plain text="" preferred="">>