Bacillus (Geobacillus) stearothermophilus Genome Sequencing - Strain 10

Bacillus (Geobacillus) stearothermophilus Strain 10 is being sequenced by Sharon Lewis, a graduate student in our laboratory at the University of Oklahoma, Norman Campus's Advanced Center for Genome Technology, in the Department of Chemistry and Biochemistry, which is funded in part by an NSF EPSCoR grant


Lineage : Bacteria; Firmicutes; Bacilli; Bacillales; unclassified Bacillales; Geobacillus stearothermophilus

Bacillus (Geobacillus) stearothermophilus Genome Sequencing Progress

  • To date, we now are sequencing individual, shotgun-based, double stranded templates generated from a randomly sheared library of the Bacillus (Geobacillus) stearothermophilus genome, with both the universal forward and reverse pUC sequencing primers.
  • We now are including all contigs longer than 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.
  • As of 12-8-97, all our data releases have been automated.
  • As of 10-29-98 we switched to Phred980904.a and Phrap980831 and also increased our database assembly stringency from the default values of PHRAP's min_match and min_score by doubling them to produce high stringency assembled data that is more accurate.

  • View the Latest Phrap High Stringency Bacillus (Geobacillus) stearothermophilus Statistics

  • Search the Bacillus (Geobacillus) stearothermophilus Genome sequence data using Blastall


    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

    If you have determined which contig is of interest to you using the above Blast search capability on the OU Server, this contig(s) are in the 'bstearo-2k.fa' file or the 'contigs-2k' directory on our ftp site.

    If however, you determined which contig was of interest using the 'KeyWord Search' option, then the contig(s) of interest will be found in the 'bstearo_weekly-2k.fa' file or the 'contigs_weekly-2k' directory

  • Obtaining the Bacillus (Geobacillus) stearothermophilus Sequencing Data via ftp
    If the above link does not work, please try:
  • Obtaining the Bacillus (Geobacillus) stearothermophilus Sequencing Data via alternative ftp

  • If instead, you would rather ftp this file directly, you can ftp to ftp.bstearo.ou.edu (logon as anonymous with password your e-mail address). Read the 00readme file in the ftp directory to determine which files you are interested in.

    Clone Availability

  • The Bacillus (Geobacillus) stearothermophilus - Strain 10 being sequenced, has been submitted to the ATCC but because of restrictions by the National Park Service cannot be distributed by the ATCC.
  • We therefore have submitted this strain to the German Collection of Microorganisms and Cell Cultures and it is cataloged under DSM 13240.
  • 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. Stenesh, B.A. Roe and T.L. Snyder. Studies of the DNA from Mesophilic and Thermophilic Bacteria. Biochem. Biophys. Acta. 161, 442-454 (1968).
  • J. Stenesh and B.A. Roe. DNA Polymerase from Mesophilic and the Thermophilic Bacteria II - Nearest Neighbor Frequency Analysis of the Products of the Reaction Catalyzed by DNA Polymerase. Biochem. Biophys. Acta. 272, 167-178 (1972).
  • J. Stenesh and B.A. Roe. DNA Polymerase from Mesophilic and Thermophilic Bacteria I- Purification and Properties of the Enzyme. Biochem. Biophys. Acta. 272, 156-166 (1972).
  • Nazina TN, Tourova TP, Poltaraus AB, Novikova EV, Grigoryan AA, Ivanova AE, Lysenko AM, Petrunyaka VV, Osipov GA, Belyaev SS, Ivanov MV. Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus (Geobacillus) stearothermophilus, Bacillus (Geobacillus) thermocatenulatus, Bacillus (Geobacillus) thermoleovorans, Bacillus (Geobacillus) kaustophilus, Bacillus (Geobacillus) thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus (Geobacillus) 6. PubMed#11321089

    Acknowledgment

    Should you find this data useful and wish to reference it, please acknowledge the Bacillus (Geobacillus) stearothermophilus Genome Sequencing Project funded by NSF EPSCoR Program (Experimental Program to Stimulate Competitive Research Grant #EPS-9550478.

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

    Thanks, Bruce Roe, Sharon Lewis, Beth Perry, Fares Najar, and Rose Morales-Diaz.
    The University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019

    Bruce Roe, broe@ou.edu

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    Bruce Roe, broe@ou.edu