\HeaderA{Athaliana}{Arabidopsis thaliana full genome (TAIR version from January 22, 2004)}{Athaliana}
\aliasA{BSgenome.Athaliana.TAIR.01222004}{Athaliana}{BSgenome.Athaliana.TAIR.01222004}
\aliasA{BSgenome.Athaliana.TAIR.01222004-package}{Athaliana}{BSgenome.Athaliana.TAIR.01222004.Rdash.package}
\keyword{package}{Athaliana}
\keyword{data}{Athaliana}
\begin{Description}\relax
Arabidopsis thaliana full genome as provided by TAIR (snapshot from January 22, 2004) and stored in Biostrings objects.
\end{Description}
\begin{Note}\relax
This BSgenome data package was made from the following source data files:
\begin{alltt}
ATH1\_chr1.1con.01222004
ATH1\_chr2.1con.01222004
ATH1\_chr3.1con.01222004
ATH1\_chr4.1con.01222004
ATH1\_chr5.1con.01222004
mitochondrial\_genomic\_sequence
ATH1\_chloroplast.1con.01072002
from ftp://ftp.arabidopsis.org/home/tair/Sequences/whole\_chromosomes/OLD/

\end{alltt}
See \code{?\LinkA{BSgenomeForge}{BSgenomeForge}} and the BSgenomeForge
vignette (\code{vignette("BSgenomeForge")}) in the BSgenome software
package for how to make a BSgenome data package.
\end{Note}
\begin{Author}\relax
H. Pages
\end{Author}
\begin{SeeAlso}\relax
\LinkA{BSgenome-class}{BSgenome.Rdash.class},
\LinkA{DNAString-class}{DNAString.Rdash.class},
\code{\LinkA{available.genomes}{available.genomes}},
\LinkA{BSgenomeForge}{BSgenomeForge}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
Athaliana
seqlengths(Athaliana)
Athaliana$chr1  # same as Athaliana[["chr1"]]

if ("AGAPS" %in% masknames(Athaliana)) {

  ## 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"])
    af <- alphabetFrequency(seq)
    found_letters <- names(af)[af != 0]
    if (any(found_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(Athaliana)) {
    cat("Checking sequence", seqname, "... ")
    seq <- Athaliana[[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")
\end{ExampleCode}
\end{Examples}

