\name{BSgenome.Celegans.UCSC.ce10}
\docType{package}

\alias{BSgenome.Celegans.UCSC.ce10-package}
\alias{BSgenome.Celegans.UCSC.ce10}
\alias{Celegans}

\title{Full genome sequences for Caenorhabditis elegans (UCSC version ce10)}

\description{
  Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce10, Oct. 2010) and stored in Biostrings objects.
}

\details{
  
}

\note{
  This BSgenome data package was made from the following source data files:
  \preformatted{
chromFa.tar.gz from ftp://hgdownload.cse.ucsc.edu/goldenPath/ce10/bigZips/
  }

  See \code{?\link[BSgenome]{BSgenomeForge}} and the BSgenomeForge
  vignette (\code{vignette("BSgenomeForge")}) in the \pkg{BSgenome}
  software package for how to make a BSgenome data package.
}

\author{The Bioconductor Dev Team}

\seealso{
  \itemize{
    \item \link[BSgenome]{BSgenome} objects and the
          \code{\link[BSgenome]{available.genomes}} function
          in the \pkg{BSgenome} software package.
    \item \link[Biostrings]{DNAString} objects in the \pkg{Biostrings}
          package.
    \item The BSgenomeForge vignette (\code{vignette("BSgenomeForge")})
          in the \pkg{BSgenome} software package for how to make a BSgenome
          data package.
  }
}

\examples{
BSgenome.Celegans.UCSC.ce10
genome <- BSgenome.Celegans.UCSC.ce10
seqlengths(genome)
genome$chrI  # same as genome[["chrI"]]

## ---------------------------------------------------------------------	## Upstream sequences
## ---------------------------------------------------------------------
## Starting with BioC 3.0, the upstream1000, upstream2000, and
## upstream5000 sequences for ce10 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("ce10", "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")
}

\keyword{package}
\keyword{data}
