Ecoli {BSgenome.Ecoli.NCBI.20080805} | R Documentation

## 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.

### Details

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):

  Escherichia coli 536

      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

  Escherichia coli APEC O1

      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

  Escherichia coli ATCC 8739

      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

  Escherichia coli CFT073

      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

  Escherichia coli E24377A

      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

  Escherichia coli HS

      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

  Escherichia coli O157:H7 EDL933

      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

  Escherichia coli O157:H7 str. Sakai

      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

  Escherichia coli SMS-3-5

      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

  Escherichia coli UTI89

      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

  Escherichia coli str. K12 substr. DH10B

      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

  Escherichia coli str. K12 substr. MG1655

      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

  Escherichia coli str. K12 substr. W3110

      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

### Note

This BSgenome data package was made from the following source data files:

    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)

See `?BSgenomeForge` and the BSgenomeForge vignette (`vignette("BSgenomeForge")`) in the BSgenome software package for how to make a BSgenome data package.

### Author(s)

H. Pages

### See Also

BSgenome-class, DNAString-class, `available.genomes`, BSgenomeForge

### Examples

    ## 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")

[Package BSgenome.Ecoli.NCBI.20080805 version 1.3.11 Index]