\name{Mmusculus}
\docType{package}

\alias{BSgenome.Mmusculus.UCSC.mm10-package}
\alias{BSgenome.Mmusculus.UCSC.mm10}
\alias{Mmusculus}


\title{Mus musculus (Mouse) full genome (UCSC version mm10)}

\description{
  Mus musculus (Mouse) full genome as provided by UCSC (mm10, Dec. 2011) and stored in Biostrings objects.
}

\details{
  
}

\note{
  This BSgenome data package was made from the following source data files:
  \preformatted{
sequences: chr1.fa.gz chr2.fa.gz chr3.fa.gz chr4.fa.gz chr5.fa.gz chr6.fa.gz chr7.fa.gz chr8.fa.gz chr9.fa.gz chr10.fa.gz chr11.fa.gz chr12.fa.gz chr13.fa.gz chr14.fa.gz chr15.fa.gz chr16.fa.gz chr17.fa.gz chr18.fa.gz chr19.fa.gz chrX.fa.gz chrY.fa.gz chrM.fa.gz chr1_GL456210_random.fa.gz chr1_GL456211_random.fa.gz chr1_GL456212_random.fa.gz chr1_GL456213_random.fa.gz chr1_GL456221_random.fa.gz chr4_GL456216_random.fa.gz chr4_GL456350_random.fa.gz chr4_JH584292_random.fa.gz chr4_JH584293_random.fa.gz chr4_JH584294_random.fa.gz chr4_JH584295_random.fa.gz chr5_GL456354_random.fa.gz chr5_JH584296_random.fa.gz chr5_JH584297_random.fa.gz chr5_JH584298_random.fa.gz chr5_JH584299_random.fa.gz chr7_GL456219_random.fa.gz chrX_GL456233_random.fa.gz chrY_JH584300_random.fa.gz chrY_JH584301_random.fa.gz chrY_JH584302_random.fa.gz chrY_JH584303_random.fa.gz chrUn_GL456239.fa.gz chrUn_GL456359.fa.gz chrUn_GL456360.fa.gz chrUn_GL456366.fa.gz chrUn_GL456367.fa.gz chrUn_GL456368.fa.gz chrUn_GL456370.fa.gz chrUn_GL456372.fa.gz chrUn_GL456378.fa.gz chrUn_GL456379.fa.gz chrUn_GL456381.fa.gz chrUn_GL456382.fa.gz chrUn_GL456383.fa.gz chrUn_GL456385.fa.gz chrUn_GL456387.fa.gz chrUn_GL456389.fa.gz chrUn_GL456390.fa.gz chrUn_GL456392.fa.gz chrUn_GL456393.fa.gz chrUn_GL456394.fa.gz chrUn_GL456396.fa.gz chrUn_JH584304.fa.gz
from http://hgdownload.cse.ucsc.edu/goldenPath/mm10/chromosomes/
AGAPS masks: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/gap.txt.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}