Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique
Kaiser O, Bartels D, Bekel T, Goesmann A, Kespohl S, Pühler A, Meyer F (2003)
JOURNAL OF BIOTECHNOLOGY 106(2-3): 121-133.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Kaiser, O.;
Bartels, D.;
Bekel, ThomasUniBi;
Goesmann, AlexanderUniBi 
;
Kespohl, S.;
Pühler, AlfredUniBi ;
Meyer, F.
;
Kespohl, S.;
Pühler, AlfredUniBi ;
Meyer, F.Einrichtung
Abstract / Bemerkung
While the sequencing of bacterial genomes has become a routine procedure at major sequencing centers, there are still a number of genome projects at small- or medium-size facilities. For these facilities a maximum of control over sequencing, assembling and finishing is essential. At the same time, facilities have to be able to co-operate at minimum costs for the overall project. We have established a pipeline for the distributed sequencing of Alcanivorax borkumensis SK2, Azoarcus sp. BH72, Clavibacter michiganensis subsp. michiganensis NCPPB382, Sorangium cellulosum So ce56 and Xanthomonas campestris pv. vesicatoria 85-10. Our pipeline relies on standard tools (e.g. PHRED/PHRAP, CAP3 and Consed/Autofinish) wherever possible, supplementing them with new tools (BioMake and BACCardI) to achieve the aims described above. (C) 2003 Elsevier B.V. All rights reserved.
Stichworte
Lander-Waterman;
Alcanivorax;
Clavibacter;
Sorangium;
Xanthomonas;
BAC;
Azoarcus;
genome project;
sequencing strategy;
assembly
Erscheinungsjahr
2003
Zeitschriftentitel
JOURNAL OF BIOTECHNOLOGY
Band
106
Ausgabe
2-3
Seite(n)
121-133
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/1609251
Zitieren
Kaiser O, Bartels D, Bekel T, et al. Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY. 2003;106(2-3):121-133.
Kaiser, O., Bartels, D., Bekel, T., Goesmann, A., Kespohl, S., Pühler, A., & Meyer, F. (2003). Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY, 106(2-3), 121-133. https://doi.org/10.1016/j.jbiotec.2003.08.008
Kaiser, O., Bartels, D., Bekel, Thomas, Goesmann, Alexander, Kespohl, S., Pühler, Alfred, and Meyer, F. 2003. “Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique”. JOURNAL OF BIOTECHNOLOGY 106 (2-3): 121-133.
Kaiser, O., Bartels, D., Bekel, T., Goesmann, A., Kespohl, S., Pühler, A., and Meyer, F. (2003). Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY 106, 121-133.
Kaiser, O., et al., 2003. Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY, 106(2-3), p 121-133.
O. Kaiser, et al., “Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique”, JOURNAL OF BIOTECHNOLOGY, vol. 106, 2003, pp. 121-133.
Kaiser, O., Bartels, D., Bekel, T., Goesmann, A., Kespohl, S., Pühler, A., Meyer, F.: Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY. 106, 121-133 (2003).
Kaiser, O., Bartels, D., Bekel, Thomas, Goesmann, Alexander, Kespohl, S., Pühler, Alfred, and Meyer, F. “Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique”. JOURNAL OF BIOTECHNOLOGY 106.2-3 (2003): 121-133.
14 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
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Shotgun sequencing of the negative-sense RNA genome of the rhabdovirus Maize mosaic virus.
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Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M., Proc. Natl. Acad. Sci. U.S.A. 89(18), 1992
PMID: 1528894
Modeling the feasibility of whole genome shotgun sequencing using a pairwise end strategy.
Siegel AF, van den Engh G, Hood L, Trask B, Roach JC., Genomics 68(3), 2000
PMID: 10995565
Siegel AF, van den Engh G, Hood L, Trask B, Roach JC., Genomics 68(3), 2000
PMID: 10995565
Strategy to sequence the genome of Corynebacterium glutamicum ATCC 13032: use of a cosmid and a bacterial artificial chromosome library.
Tauch A, Homann I, Mormann S, Ruberg S, Billault A, Bathe B, Brand S, Brockmann-Gretza O, Ruckert C, Schischka N, Wrenger C, Hoheisel J, Mockel B, Huthmacher K, Pfefferle W, Puhler A, Kalinowski J., J. Biotechnol. 95(1), 2002
PMID: 11879709
Tauch A, Homann I, Mormann S, Ruberg S, Billault A, Bathe B, Brand S, Brockmann-Gretza O, Ruckert C, Schischka N, Wrenger C, Hoheisel J, Mockel B, Huthmacher K, Pfefferle W, Puhler A, Kalinowski J., J. Biotechnol. 95(1), 2002
PMID: 11879709
AUTHOR UNKNOWN, 0
Complete nucleotide sequence of two generations of a bacterial artificial chromosome cloning vector.
Wang K, Boysen C, Shizuya H, Simon MI, Hood L., BioTechniques 23(6), 1997
PMID: 9421622
Wang K, Boysen C, Shizuya H, Simon MI, Hood L., BioTechniques 23(6), 1997
PMID: 9421622
The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti.
Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorholter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J, Golding B, Puhler A., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
PMID: 11481431
Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorholter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J, Golding B, Puhler A., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
PMID: 11481431
Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium.
Yakimov MM, Golyshin PN, Lang S, Moore ER, Abraham WR, Lunsdorf H, Timmis KN., Int. J. Syst. Bacteriol. 48 Pt 2(), 1998
PMID: 9731272
Yakimov MM, Golyshin PN, Lang S, Moore ER, Abraham WR, Lunsdorf H, Timmis KN., Int. J. Syst. Bacteriol. 48 Pt 2(), 1998
PMID: 9731272
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