Hi all, Is there a way to fetch genomic sequences via Bioconductor directly? (Using galaxy, but I would like to automate) I tried rtracklayer and biomaRt - rtracklayer doesn't seem to have an interface for fetching sequences, and biomaRt only seems to fetch sequences from a subset of gene ID's, while I just to need to fetch sequence from a genomic range. fetchSequence(chr, strand, start, end) -> sequence Any suggestions? Thank you in advance!! Best regards, JW, Uni. of Copenhagen [[alternative HTML version deleted]]

Hi Johannes, I thought 'getSequence' from the biomaRt package should allow you to do what you want. But, I can't seem to get it to work for genomic coordinates either: library(biomaRt) ens <- useMart("ensembl","hsapiens_gene_ensembl") getSequence(chromosome=1,start=10000,end=11000, seqType="genomic", mart=ens) Error in getSequence(chromosome = 1, start = 10000, end = 11000, seqType = "genomic", : Please specify the type of sequence that needs to be retrieved when using biomaRt in web service mode. Choose either gene_exon, transcript_exon,transcript_exon_intron, gene_exon_intron, cdna, coding,coding_transcript_flank,coding_gene_flank,transcript_flank,gene _flank,peptide, 3utr or 5utr > sessionInfo() R version 2.10.0 (2009-10-26) i386-apple-darwin9.8.0 locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] tools stats graphics grDevices datasets utils methods [8] base other attached packages: [1] biomaRt_2.2.0 Biobase_2.6.0 loaded via a namespace (and not attached): [1] RCurl_1.2-1 XML_2.6-0 Cheers, Cei Johannes Waage wrote: > Hi all, > > Is there a way to fetch genomic sequences via Bioconductor directly? (Using > galaxy, but I would like to automate) > > I tried rtracklayer and biomaRt - rtracklayer doesn't seem to have an > interface for fetching sequences, and biomaRt only seems to fetch sequences > from a subset of gene ID's, while I just to need to fetch sequence from a > genomic range. > > fetchSequence(chr, strand, start, end) -> sequence > > Any suggestions? > > Thank you in advance!! > > Best regards, > JW, > Uni. of Copenhagen > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

Ah, simple but perfect. Thanks! /JW On Mon, Jan 11, 2010 at 11:15 AM, Paul Leo <p.leo@uq.edu.au> wrote: > If you have a bed file then all you need are the BSgemome.* packages to > get the sequences .... > > library("BSgenome.Mmusculus.UCSC.mm9") > all.genomic<-getSeq(Mmusculus, the.chrom, starts, ends) > > where > the.chrom[1:5] > [1] "chr1" "chr1" "chr1" "chr1" "chr1"' > starts[1:5] > 3187526 3487463 3777276 4144186 4274111 > > ends[1:5] > [1] 3187790 3487763 3777555 4144499 4274416 > > > etc etc... > myb<-"YAACKG" > length(all.genomic) > system.time(x<- XStringViews(all.genomic, "DNAString")) > x.labels<-paste(the.chrom,starts,ends,sep=":") > names(x)<-x.labels > ###################### forward counts ################# > all.matches<-matchPattern(myb.dna,x,max.mismatch=0, fixed=FALSE) # needs > a stringView to vectorize > the.cov<-coverage(all.matches) > > counts<-aggregate(the.cov,start=start(x),end=end(x),FUN=sum)/length( myb.dna) > ###################################################### > > -----Original Message----- > From: Johannes Waage <johannes.waage@bric.dk> > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] Get genomic sequences > Date: Mon, 11 Jan 2010 10:56:21 +0100 > > Hi all, > > Is there a way to fetch genomic sequences via Bioconductor directly? (Using > galaxy, but I would like to automate) > > I tried rtracklayer and biomaRt - rtracklayer doesn't seem to have an > interface for fetching sequences, and biomaRt only seems to fetch sequences > from a subset of gene ID's, while I just to need to fetch sequence from a > genomic range. > > fetchSequence(chr, strand, start, end) -> sequence > > Any suggestions? > > Thank you in advance!! > > Best regards, > JW, > Uni. of Copenhagen > > [[alternative HTML version deleted]] > > _______________________________________________ > 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]]

If you have a bed file then all you need are the BSgenome.* packages to get the sequences .... library("BSgenome.Mmusculus.UCSC.mm9") all.genomic<-getSeq(Mmusculus, the.chrom, starts, ends) where the.chrom[1:5] [1] "chr1" "chr1" "chr1" "chr1" "chr1"' starts[1:5] 3187526 3487463 3777276 4144186 4274111 > ends[1:5] [1] 3187790 3487763 3777555 4144499 4274416 etc etc... myb<-"YAACKG" length(all.genomic) system.time(x<- XStringViews(all.genomic, "DNAString")) x.labels<-paste(the.chrom,starts,ends,sep=":") names(x)<-x.labels ###################### forward counts ################# all.matches<-matchPattern(myb.dna,x,max.mismatch=0, fixed=FALSE) # needs a stringView to vectorize the.cov<-coverage(all.matches) counts<-aggregate(the.cov,start=start(x),end=end(x),FUN=sum)/length(my b.dna) ###################################################### -----Original Message----- From: Johannes Waage <johannes.waage@bric.dk> To: bioconductor at stat.math.ethz.ch Subject: [BioC] Get genomic sequences Date: Mon, 11 Jan 2010 10:56:21 +0100 Hi all, Is there a way to fetch genomic sequences via Bioconductor directly? (Using galaxy, but I would like to automate) I tried rtracklayer and biomaRt - rtracklayer doesn't seem to have an interface for fetching sequences, and biomaRt only seems to fetch sequences from a subset of gene ID's, while I just to need to fetch sequence from a genomic range. fetchSequence(chr, strand, start, end) -> sequence Any suggestions? Thank you in advance!! Best regards, JW, Uni. of Copenhagen [[alternative HTML version deleted]] _______________________________________________ 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