\HeaderA{Ecoli}{Escherichia coli full genomes}{Ecoli}
\aliasA{BSgenome.Ecoli.NCBI.20080805}{Ecoli}{BSgenome.Ecoli.NCBI.20080805}
\aliasA{BSgenome.Ecoli.NCBI.20080805-package}{Ecoli}{BSgenome.Ecoli.NCBI.20080805.Rdash.package}
\keyword{package}{Ecoli}
\keyword{data}{Ecoli}
\begin{Description}\relax
Escherichia coli full genomes for several strains as provided by NCBI on 2008/08/05 and stored in Biostrings objects.
\end{Description}
\begin{Details}\relax
The genome of Escherichia coli is made of a single circular DNA sequence.
The full genomes for the following strains are present in
this package (one sequence per strain):
\describe{
\item[] Escherichia coli 536
\begin{alltt}
Taxonomy ID: 362663
Other names: Escherichia coli strain 536, Escherichia coli str. 536
Refseq: NC\_008253
Length: 4,938,920 nt
Seq.Status: Completed
Sequencing center: University of Goettingen
Completed: 2006/07/24
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_536/NC\_008253.fna
\end{alltt}
\item[] Escherichia coli APEC O1
\begin{alltt}
Taxonomy ID: 405955
Other names: Escherichia coli strain APEC O1, Escherichia coli str. APEC O1
Refseq: NC\_008563
Length: 5,082,025 nt
Seq.Status: Completed
Sequencing center: Iowa State University
Completed: 2006/11/08
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_APEC\_O1/NC\_008563.fna
\end{alltt}
\item[] Escherichia coli ATCC 8739
\begin{alltt}
Taxonomy ID: 481805
Other names: Escherichia coli C (ATCC 8739), Escherichia coli C str. ATCC 8739, Escherichia coli strain ATCC 8739, Escherichia coli str. ATCC 8739
Refseq: NC\_010468
Length: 4,746,218 nt
Seq.Status: Completed
Sequencing center: US DOE Joint Genome Institute (JGI-PGF)
Completed: 2008/03/17
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_C\_ATCC\_8739/NC\_010468.fna
\end{alltt}
\item[] Escherichia coli CFT073
\begin{alltt}
Taxonomy ID: 199310
Other names: Escherichia coli strain CFT073,
Escherichia coli str. CFT073
Refseq: NC\_004431
Length: 5,231,428 nt
Seq.Status: Completed
Sequencing center: Univ. Wisconsin
Completed: 2002/12/09
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_CFT073/NC\_004431.fna
\end{alltt}
\item[] Escherichia coli E24377A
\begin{alltt}
Taxonomy ID: 331111
Refseq: NC\_009801
Length: 4,979,619 nt
Seq.Status: Completed
Sequencing center: TIGR
Completed: 2007/09/13
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_E24377A/NC\_009801.fna
\end{alltt}
\item[] Escherichia coli HS
\begin{alltt}
Taxonomy ID: 331112
Refseq: NC\_009800
Length: 4,643,538 nt
Seq.Status: Completed
Sequencing center: TIGR
Completed: 2007/09/13
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_HS/NC\_009800.fna
\end{alltt}
\item[] Escherichia coli O157:H7 EDL933
\begin{alltt}
Taxonomy ID: 155864
Refseq: NC\_002655
Length: 5,528,445 nt
Seq.Status: Completed
Sequencing center: Univ. Wisconsin
Completed: 2001/09/27
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_O157H7\_EDL933/NC\_002655.fna
\end{alltt}
\item[] Escherichia coli O157:H7 str. Sakai
\begin{alltt}
Taxonomy ID: 386585
Other names: Escherichia coli O157:H7 strain Sakai
Refseq: NC\_002695
Length: 5,498,450 nt
Seq.Status: Completed
Sequencing center: GIRC
Completed: 2001/10/02
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_O157H7/NC\_002695.fna
\end{alltt}
\item[] Escherichia coli SMS-3-5
\begin{alltt}
Taxonomy ID: 439855
Other names: Escherichia coli strain SMS-3-5, Escherichia coli str. SMS-3-5
Refseq: NC\_010498
Length: 5,068,389 nt
Seq.Status: Completed
Sequencing center: TIGR
Completed: 2008/03/24
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_SMS\_3\_5/NC\_010498.fna
\end{alltt}
\item[] Escherichia coli UTI89
\begin{alltt}
Taxonomy ID: 364106
Other names: Escherichia coli strain UTI89, Escherichia coli str. UTI89
Refseq: NC\_007946
Length: 5,065,741 nt
Seq.Status: Completed
Sequencing center: Washington University (WashU)
Completed: 2006/04/07
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_UTI89/NC\_007946.fna
\end{alltt}
\item[] Escherichia coli str. K12 substr. DH10B
\begin{alltt}
Taxonomy ID: 316385
Other names: Escherichia coli DH10B, Escherichia coli strain K12 substrain DH10B
Refseq: NC\_010473
Length: 4,686,137 nt
Seq.Status: Completed
Sequencing center: University of Wisconsin-Madison
Completed: 2008/03/17
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_K\_12\_substr\_\_DH10B/NC\_010473.fna
\end{alltt}
\item[] Escherichia coli str. K12 substr. MG1655
\begin{alltt}
Taxonomy ID: 511145
Other names: Escherichia coli MG1655, Escherichia coli strain MG1655, Escherichia coli str. MG1655
Refseq: NC\_000913
Length: 4,639,675 nt
Seq.Status: Completed
Sequencing center: Univ. Wisconsin
Completed: 2001/10/15
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_K12\_substr\_\_MG1655/NC\_000913.fna
\end{alltt}
\item[] Escherichia coli str. K12 substr. W3110
\begin{alltt}
Taxonomy ID: 316407
Other names: Escherichia coli W3110, Escherichia coli strain W3110, Escherichia coli str. W3110
Refseq: AC\_000091
Length: 4,646,332 nt
Seq.Status: Completed
Sequencing center: Nara Institute of Science and Technology
Completed: 2006/03/01
File: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia\_coli\_W3110/AC\_000091.fna
\end{alltt}
}
\end{Details}
\begin{Note}\relax
This BSgenome data package was made from the following source data files:
\begin{alltt}
Escherichia\_coli\_536/NC\_008253.fna
Escherichia\_coli\_APEC\_O1/NC\_008563.fna
Escherichia\_coli\_C\_ATCC\_8739/NC\_010468.fna
Escherichia\_coli\_CFT073/NC\_004431.fna
Escherichia\_coli\_E24377A/NC\_009801.fna
Escherichia\_coli\_HS/NC\_009800.fna
Escherichia\_coli\_O157H7\_EDL933/NC\_002655.fna
Escherichia\_coli\_O157H7/NC\_002695.fna
Escherichia\_coli\_SMS\_3\_5/NC\_010498.fna
Escherichia\_coli\_UTI89/NC\_007946.fna
Escherichia\_coli\_K\_12\_substr\_\_DH10B/NC\_010473.fna
Escherichia\_coli\_K12\_substr\_\_MG1655/NC\_000913.fna
Escherichia\_coli\_W3110/AC\_000091.fna
from ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ (downloaded on 2008/08/05)

\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}
## The names of the sequences are the Refseq numbers:
Ecoli
seqlengths(Ecoli)
Ecoli$NC_008253  # same as Ecoli[["NC_008253"]]

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

  ## 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(Ecoli)) {
    cat("Checking sequence", seqname, "... ")
    seq <- Ecoli[[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}

