Depending on what you know (start positions etc) - Biostrings is a reasonable tool for extracting these in an efficient manner - a number of genomes are available now, and more can be added Steffen Durinck wrote: > No, I don't think there is a package to find motifs in the current > repository. > It would be nice to have one. > > best, > Steffen > > Henrik Hornsh?j Jensen wrote: >> Thanks for your help, although I was thinking of a bioconductor package. >> >> Regards, >> Henrik >> >> >> >> -----Oprindelig meddelelse----- >> Fra: Krys Kelly [mailto:kak28 at cam.ac.uk] >> Sendt: Tuesday, September 19, 2006 12:35 PM >> Til: Henrik Hornsh?j Jensen; bioconductor at stat.math.ethz.ch >> Emne: RE: [BioC] retrieving upstream/intronic sequences using biomaRt >> >> Hi Henrik, >> >> A package? The more one looks, the more one finds! The attached spreadsheet is very much a work in progress and a bit messy and incomplete. >> We started it after a very quick review of the literature, so it is also far from comprehensive. However, it will probably give you more than enough information to get started. >> >> This review should be helpful: >> >> Tompa et al (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology 23(1) 137-144. >> >> The three 'old-timer' programs that everyone seems to use are AlignACE, Meme and Consensus. And we have also been using Weeder, Sombrero and NestedMica. >> Be aware that some of the programs (e.g. AlignACE) can give quite different answers on different runs even with the same parameters. And the different programs can give very different answers. I am aware that a number of people (including ourselves) use several of the programs and take the motifs that turn up in most of the programs for further study. >> >> There are also programs that search for known motifs (e.g. MAST (companion to MEME), MSCAN, SiteSeer). Two well-known databases of Transcription Factor Binding Sites are TRANSFAC and JASPAR. >> >> Hope this helps. >> >> Krys >> >> >> Dr Krystyna A Kelly >> University of Cambridge >> Department of Pathology >> Molteno Building, Tennis Court Road >> Cambridge CB2 1QP >> Tel: 01223 333331 >> Email: kak28 at cam.ac.uk >> >> >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch >> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Henrik Hornsh?j Jensen >> Sent: 19 September 2006 10:33 >> To: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] retrieving upstream/intronic sequences using biomaRt >> >> Any of you guys know a package that will predict regulatory sites in upstream regions? >> >> Regards, >> Henrik >> >> >> >> -----Oprindelig meddelelse----- >> Fra: bioconductor-bounces at stat.math.ethz.ch >> [mailto:bioconductor-bounces at stat.math.ethz.ch] P? vegne af Steffen Durinck >> Sendt: Wednesday, September 13, 2006 2:25 PM >> Til: Shamit Soneji >> Cc: BioC >> Emne: Re: [BioC] retrieving upstream/intronic sequences using biomaRt >> >> Hi Shamit, >> >> Yes, with biomaRt you can get the upstream sequences but currently not the intronic sequences. >> Try: >> >> library(biomaRt) >> ensmart = useMart("ensembl",dataset="hsapiens_gene_ensembl") >> getSequence( id="ENSG00000139618", type="ensembl",mart = ensmart, seqType = >> "5utr") >> >> Cheers, >> Steffen >> >> >> Shamit Soneji wrote: >> >>> Is it possible using biomaRt (or any other R/BioC means) to download >>> the upstream and intron sequences for any given ensembl ID? >>> >>> I know this can be done just using straight biomart, but a facility >>> like this from R would be very useful if one wants to search for TF >>> binding sites. >>> >>> Many thanks >>> >>> Shamit >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org