\name{Mmusculus} \docType{package} \alias{BSgenome.Mmusculus.UCSC.mm8-package} \alias{BSgenome.Mmusculus.UCSC.mm8} \alias{Mmusculus} \title{Mus musculus (Mouse) full genome (UCSC version mm8)} \description{ Mus musculus (Mouse) full genome as provided by UCSC (mm8, Feb. 2006) and stored in Biostrings objects. } \details{ } \note{ This BSgenome data package was made from the following source data files: \preformatted{ sequences: chromFa.tar.gz, upstream1000.fa.gz, upstream2000.fa.gz, upstream5000.fa.gz from http://hgdownload.cse.ucsc.edu/goldenPath/mm8/bigZips/ AGAPS masks: all the chr*_gap.txt.gz files from ftp://hgdownload.cse.ucsc.edu/goldenPath/mm8/database/ RM masks: http://hgdownload.cse.ucsc.edu/goldenPath/mm8/bigZips/chromOut.tar.gz TRF masks: http://hgdownload.cse.ucsc.edu/goldenPath/mm8/bigZips/chromTrf.tar.gz } See \code{?\link[BSgenome]{BSgenomeForge}} and the BSgenomeForge vignette (\code{vignette("BSgenomeForge")}) in the BSgenome software package for how to make a BSgenome data package. } \author{H. Pages} \seealso{ \link[BSgenome]{BSgenome-class}, \link[Biostrings]{DNAString-class}, \code{\link[BSgenome]{available.genomes}}, \link[BSgenome]{BSgenomeForge} } \examples{ Mmusculus seqlengths(Mmusculus) Mmusculus$chr1 # same as Mmusculus[["chr1"]] if ("AGAPS" \%in\% masknames(Mmusculus)) { ## Check that the assembly gaps contain only Ns: checkOnlyNsInGaps <- function(seq) { ## Replace all masks by the inverted AGAPS mask masks(seq) <- gaps(masks(seq)["AGAPS"]) unique_letters <- uniqueLetters(seq) if (any(unique_letters != "N")) stop("assembly gaps contain more than just Ns") } ## A message will be printed each time a sequence is removed ## from the cache: options(verbose=TRUE) for (seqname in seqnames(Mmusculus)) { cat("Checking sequence", seqname, "... ") seq <- Mmusculus[[seqname]] checkOnlyNsInGaps(seq) cat("OK\n") } } ## 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") } \keyword{package} \keyword{data}