Neisseria gonorrhoeae Genome Sequencing - Strain FA 1090


Neisseria gonorrhoeae Genome Sequencing Progress

As of 12-8-97, our data release has been automated. Therefore, we expect to release our data at least twice a week as we obtain the closure and proofreading data.
  • To date, we have sequenced over 12,480 individual, shotgun-based, double stranded templates generated from a randomly sheared library of the Neisseria gonorrhoeae genome, with both the universal forward and reverse pUC sequencing primers.
  • Over 14 million bases of sequence have been collected and aligned into a database containing over 2M unique bases. This represents over 97% of the sequence of the entire Neisseria gonorrhoeae genome.
  • We now are including all contigs >1kb because much of the data in the 1-2kb contig may be useful as it now has multiple sequence reads.
  • The data in contigs that are shorter than 1kb still is highly inaccurate and not included in this release.
  • Should you desire the shorter than 1kb data, please contact me and we will make it available to you.
  • Please note that we continue to represent lower confidence data in lower case letters.
  • Should you desire the <1kb data, please contact me and we will make it available with the next release.

  • View the latest Neisseria gonorrhoeae Statistics

  • Search the Neisseria gonorrhoeae Genome sequence data


    Obtaining the sequence data via ftp

    All of our shotgun sequence data is available via ftp (see below) but at the present time, the various contigs are in "random" order and do not correspond to any specific relationship one to another. Please be aware that the order and contig number will change with each new release of data.

    Caution: the data has been neither proof read nor edited and thus should be considered preliminary raw sequence data. Also, because the sequence assembly program, Phrap, has the tendency to include inaccurate sequence reads on the ends of contigs, be cautious when using sequences within 1-200 bases of the ends of individual contigs. Please take this into account when using this data

    As we now move on to the "closure" phase over the next few weeks, these contigs will be edited, joined, and eventually ordered.

  • Obtaining the Neisseria gonorrhoeae Sequencing Data via ftp

  • If instead, you would rather ftp this file directly, you can ftp to ftp.gono.ou.edu (logon as anonymous with password your e-mail address) . Get the ascii file gono_weekly-1k.fa that is contained in /pub/gono that contains all the contigs in one file, or get the individual contigs of interest from the contigs_weekly-1k directory.

    Clone Availability

  • The Neisseria gonorrhoeae - Strain FA 1090 being sequenced, has been submitted to the ATCC and given accession number ATCC 700294.
  • At the present time, none of the shotgun clones are available for distribution. We anticipate at some point to generate a set of ordered sub-clones that will be made available throught the ATCC.

    Literature Reference Describing Strain being sequenced

  • J.F. Dempsey, W. Litaker, A. Madhure, T.L. Snodgrass, J.G. Cannon. 1991. Physical map of the chromosome of Neisseria gonorrhoeae FA1090 with locations of genetic markers, including opa and pil genes. J. Bacteriol. 173: 5476-5486

    Acknowledgment

    Should you find this data useful and wish to reference it, please acknowledge the Gonococcal Genome Sequencing Project, and B.A. Roe, S. P. Lin, L. Song, X. Yuan, S. Clifton and D.W. Dyer; this project is supported by USPHS/NIH grant #AI38399.

    If possible, please send us both the literature citation once published, and a copy of the manuscript.

    Thanks, Bruce Roe, ShaoPing Lin, Lin Song, XiLing Yuan, Sandy Clifton and Dave Dyer.
    The University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019 and The University of Oklahoma Health Sciences Center, Department of Microbiology and Immunology, Oklahoma City, Oklahoma 73190


    Home Page

    Bruce Roe, broe@ou.edu