BSgenome.Celegans.UCSC.ce2 {BSgenome.Celegans.UCSC.ce2} | R Documentation |
Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce2, Mar. 2004) and stored in Biostrings objects.
This BSgenome data package was made from the following source data files:
chromFa.zip from http://hgdownload.cse.ucsc.edu/goldenPath/ce2/bigZips/
See ?BSgenomeForge
and the BSgenomeForge
vignette (vignette("BSgenomeForge")
) in the BSgenome
software package for how to make a BSgenome data package.
The Bioconductor Dev Team
BSgenome objects and the
available.genomes
function
in the BSgenome software package.
DNAString objects in the Biostrings package.
The BSgenomeForge vignette (vignette("BSgenomeForge")
)
in the BSgenome software package for how to make a BSgenome
data package.
BSgenome.Celegans.UCSC.ce2 genome <- BSgenome.Celegans.UCSC.ce2 seqlengths(genome) genome$chrI # same as genome[["chrI"]] ## --------------------------------------------------------------------- ## Upstream sequences ## --------------------------------------------------------------------- ## Starting with BioC 3.0, the upstream1000, upstream2000, and ## upstream5000 sequences for ce2 are not included in the BSgenome data ## package anymore. However they can easily be extracted from the full ## genome sequences with something like: library(GenomicFeatures) txdb <- makeTranscriptDbFromUCSC("ce2", "refGene") gn <- sort(genes(txdb)) up1000 <- flank(gn, width=1000) up1000seqs <- getSeq(genome, up1000) ## IMPORTANT: Make sure you use a TxDb package (or TranscriptDb object), ## that contains a gene model based on the exact same reference genome ## as the BSgenome object you pass to getSeq(). Note that you can make ## your own custom TranscriptDb object from various annotation resources. ## See the makeTranscriptDbFromUCSC(), makeTranscriptDbFromBiomart(), ## and makeTranscriptDbFromGFF() functions in the GenomicFeatures ## package. ## --------------------------------------------------------------------- ## Genome-wide motif searching ## --------------------------------------------------------------------- ## See the GenomeSearching vignette in the BSgenome software ## package for some examples of genome-wide motif searching using ## Biostrings and the BSgenome data packages: if (interactive()) vignette("GenomeSearching", package="BSgenome")