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.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
14 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
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Krause A, Ramakumar A, Bartels D, Battistoni F, Bekel T, Boch J, Böhm M, Friedrich F, Hurek T, Krause L, Linke B, McHardy AC, Sarkar A, Schneiker S, Syed AA, Thauer R, Vorhölter FJ, Weidner S, Pühler A, Reinhold-Hurek B, Kaiser O, Goesmann A., Nat Biotechnol 24(11), 2006
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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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