Ecoli      package:BSgenome.Ecoli.NCBI.20080805      R Documentation

_E_s_c_h_e_r_i_c_h_i_a _c_o_l_i _f_u_l_l _g_e_n_o_m_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Escherichia coli full genomes for several strains as provided by
     NCBI on 2008/08/05 and stored in Biostrings objects.

_D_e_t_a_i_l_s:

     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


_N_o_t_e:

     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.

_A_u_t_h_o_r(_s):

     H. Pages

_S_e_e _A_l_s_o:

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

_E_x_a_m_p_l_e_s:

     ## 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")

