Package: BSgenome.Ecoli.NCBI.20080805
Title: Escherichia coli full genomes
Description: Escherichia coli full genomes for several strains as provided by NCBI on 2008/08/05 and stored in Biostrings objects.
Version: 1.4.2
organism: Escherichia coli
common_name: E. coli
provider: NCBI
provider_version: 2008/08/05
release_date: NA
release_name: NA
source_url: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
organism_biocview: Escherichia_coli
BSgenomeObjname: Ecoli
seqnames: c(paste("NC_", c("008253", "008563", "010468", "004431", "009801", "009800", "002655", "002695", "010498", "007946", "010473", "000913"), sep=""), "AC_000091")
circ_seqs: c(paste("NC_", c("008253", "008563", "010468", "004431", "009801", "009800", "002655", "002695", "010498", "007946", "010473", "000913"), sep=""), "AC_000091")
PkgDetails: 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
	  \preformatted{
	  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
	}}
	\item{}{
	  Escherichia coli APEC O1
	  \preformatted{
	  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
	}}
	\item{}{
	  Escherichia coli ATCC 8739
	  \preformatted{
	  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
	}}
	\item{}{
	  Escherichia coli CFT073
	  \preformatted{
	  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
	}}
	\item{}{
	  Escherichia coli E24377A
	  \preformatted{
	  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
	}}
	\item{}{
	  Escherichia coli HS
	  \preformatted{
	  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
	}}
	\item{}{
	  Escherichia coli O157:H7 EDL933
	  \preformatted{
	  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
	}}
	\item{}{
	  Escherichia coli O157:H7 str. Sakai
	  \preformatted{
	  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
	}}
	\item{}{
	  Escherichia coli SMS-3-5
	  \preformatted{
	  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
	}}
	\item{}{
	  Escherichia coli UTI89
	  \preformatted{
	  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
	}}
	\item{}{
	  Escherichia coli str. K12 substr. DH10B
	  \preformatted{
	  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
	}}
	\item{}{
	  Escherichia coli str. K12 substr. MG1655
	  \preformatted{
	  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
	}}
	\item{}{
	  Escherichia coli str. K12 substr. W3110
	  \preformatted{
	  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
	}}
	}
SrcDataFiles: 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)
PkgExamples: ## The names of the sequences are the Refseq numbers!
	genome$NC_008253  # same as genome[["NC_008253"]]
seqs_srcdir: /fh/fast/morgan_m/BioC/BSgenomeForge/srcdata/BSgenome.Ecoli.NCBI.20080805/seqs
seqfiles_suffix: .fna
ondisk_seq_format: rda