Hi guys, I just wonder if there is any Bioconductor package that can take a short nucleotide sequence (25 mer) or its genomic coordinate (chr & pos) as input and return exon number it maps to? Thanks a lot for the help! Ying Chen [[alternative HTML version deleted]]

On 06/15/2012 11:08 AM, ying chen wrote: > > > > > Hi guys, I just wonder if there is any Bioconductor package that can > take a short nucleotide sequence (25 mer) or its genomic coordinate > (chr& pos) as input and return exon number it maps to? Thanks a lot Take a look at GenomicRanges / GenomicFeatures, you might read your alignments as readGappedAlignments, or just create a GRanges() object, library(GenomicRanges) reads = GRanges(c("chr1", "chr7"), IRanges(start=c(12614, 195554), width=1)) and then use a package like TxDb.Hspaiens library(TxDb.Hsapiens.UCSC.hg19.knownGene) ex = exons(TxDb.Hsapiens.UCSC.hg19.knownGene) and findOverlaps hits = findOverlaps(reads, ex) to discover that your 'query' (reads) overlaps the exons > queryHits(hits) [1] 1 1 2 > values(ex)$exon_id[subjectHits(hits)] [1] 5 2 98786 Martin > for the help! Ying Chen [[alternative HTML version deleted]] > > _______________________________________________ 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 -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793