The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies
Bekel T, Henckel K, Küster H, Meyer F, Mittard-Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, et al. (2009)
Journal of Biotechnology 140(1-2): 3-12.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Bekel, ThomasUniBi;
Henckel, KoljaUniBi;
Küster, Helge;
Meyer, Folker;
Mittard-Runte, VirginieUniBi;
Neuweger, HeikoUniBi;
Paarmann, Daniel;
Rupp, OliverUniBi;
Zakrzewski, MarthaUniBi;
Pühler, AlfredUniBi 
;
Stoye, JensUniBi ;
Goesmann, AlexanderUniBi
Alle
;
Stoye, JensUniBi ;
Goesmann, AlexanderUniBi
Alle
Einrichtung
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Technische Fakultät > Computational Genomics
Abstract / Bemerkung
DNA sequencing plays a more and more important role in various fields of genetics. This includes sequencing of whole genomes, libraries of cDNA clones and probes of metagenome communities. The applied sequencing technologies evolve permanently. With the emergence of ultrafast sequencing technologies, a new era of DNA sequencing has recently started. Concurrently, the needs for adapted bioinformatics tools arise. Since the ability to process current datasets efficiently is essential for modern genetics, a modular bioinformatics platform providing extensive sequence analysis methods, is designated to achieve well the constantly growing requirements. The Sequence Analysis and Management System (SAMS) is a bioinformatics software platform with a database backend designed to support the computational analysis of (1) whole genome shotgun (WGS) bacterial genome sequencing, (2) cDNA sequencing by reading expressed sequence tags (ESTs) as well as (3) sequence data obtained by ultrafast sequencing. It provides extensive bioinformatics analysis of sequenced single reads, sequencing libraries and fragments of arbitrary DNA sequences such as assembled contigs of metagenome reads for instance. The system has been implemented to cope with several thousands of sequences, efficiently processing them and storing the results for further analysis. With the project setup, SAMS automatically recognizes the data type.
Stichworte
DNA sequence quality control;
cDNA;
Whole genome shotgun sequencing;
sequencing;
EST clustering;
Ultrafast sequencing
Erscheinungsjahr
2009
Zeitschriftentitel
Journal of Biotechnology
Band
140
Ausgabe
1-2
Seite(n)
3-12
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/1634447
Zitieren
Bekel T, Henckel K, Küster H, et al. The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. Journal of Biotechnology. 2009;140(1-2):3-12.
Bekel, T., Henckel, K., Küster, H., Meyer, F., Mittard-Runte, V., Neuweger, H., Paarmann, D., et al. (2009). The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. Journal of Biotechnology, 140(1-2), 3-12. https://doi.org/10.1016/j.jbiotec.2009.01.006
Bekel, Thomas, Henckel, Kolja, Küster, Helge, Meyer, Folker, Mittard-Runte, Virginie, Neuweger, Heiko, Paarmann, Daniel, et al. 2009. “The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies”. Journal of Biotechnology 140 (1-2): 3-12.
Bekel, T., Henckel, K., Küster, H., Meyer, F., Mittard-Runte, V., Neuweger, H., Paarmann, D., Rupp, O., Zakrzewski, M., Pühler, A., et al. (2009). The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. Journal of Biotechnology 140, 3-12.
Bekel, T., et al., 2009. The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. Journal of Biotechnology, 140(1-2), p 3-12.
T. Bekel, et al., “The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies”, Journal of Biotechnology, vol. 140, 2009, pp. 3-12.
Bekel, T., Henckel, K., Küster, H., Meyer, F., Mittard-Runte, V., Neuweger, H., Paarmann, D., Rupp, O., Zakrzewski, M., Pühler, A., Stoye, J., Goesmann, A.: The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. Journal of Biotechnology. 140, 3-12 (2009).
Bekel, Thomas, Henckel, Kolja, Küster, Helge, Meyer, Folker, Mittard-Runte, Virginie, Neuweger, Heiko, Paarmann, Daniel, Rupp, Oliver, Zakrzewski, Martha, Pühler, Alfred, Stoye, Jens, and Goesmann, Alexander. “The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies”. Journal of Biotechnology 140.1-2 (2009): 3-12.
18 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
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Jang HJ, Yoon SH, Ryu HK, Kim JH, Wang CL, Kim JY, Oh DK, Kim SW., Microb Cell Fact 10(), 2011
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Lander ES, Waterman MS., Genomics 2(3), 1988
PMID: 3294162
ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences.
Lee B, Hong T, Byun SJ, Woo T, Choi YJ., Nucleic Acids Res. 35(Web Server issue), 2007
PMID: 17526512
Lee B, Hong T, Byun SJ, Woo T, Choi YJ., Nucleic Acids Res. 35(Web Server issue), 2007
PMID: 17526512
An optimized protocol for analysis of EST sequences.
Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J., Nucleic Acids Res. 28(18), 2000
PMID: 10982889
Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J., Nucleic Acids Res. 28(18), 2000
PMID: 10982889
Host genes involved in nodulation preference in common bean (Phaseolus vulgaris)-rhizobium etli symbiosis revealed by suppressive subtractive hybridization.
Meschini EP, Blanco FA, Zanetti ME, Beker MP, Kuster H, Puhler A, Aguilar OM., Mol. Plant Microbe Interact. 21(4), 2008
PMID: 18321191
Meschini EP, Blanco FA, Zanetti ME, Beker MP, Kuster H, Puhler A, Aguilar OM., Mol. Plant Microbe Interact. 21(4), 2008
PMID: 18321191
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform.
Nagaraj SH, Deshpande N, Gasser RB, Ranganathan S., Nucleic Acids Res. 35(Web Server issue), 2007
PMID: 17545197
Nagaraj SH, Deshpande N, Gasser RB, Ranganathan S., Nucleic Acids Res. 35(Web Server issue), 2007
PMID: 17545197
CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data.
Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Huser AT, Kalinowski J, Oehm S, Puhler A, Rahmann S, Weile J, Goesmann A., BMC Syst Biol 1(), 2007
PMID: 18034885
Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Huser AT, Kalinowski J, Oehm S, Puhler A, Rahmann S, Weile J, Goesmann A., BMC Syst Biol 1(), 2007
PMID: 18034885
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.
Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J., Bioinformatics 19(5), 2003
PMID: 12651724
Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J., Bioinformatics 19(5), 2003
PMID: 12651724
The TIGR gene indices: reconstruction and representation of expressed gene sequences.
Quackenbush J, Liang F, Holt I, Pertea G, Upton J., Nucleic Acids Res. 28(1), 2000
PMID: 10592205
Quackenbush J, Liang F, Holt I, Pertea G, Upton J., Nucleic Acids Res. 28(1), 2000
PMID: 10592205
The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology.
Schluter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Kromeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Puhler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehover P, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18597880
Schluter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Kromeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Puhler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehover P, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18597880
Complete genome sequence of the myxobacterium Sorangium cellulosum.
Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L, Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T, Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy AC, Merai M, Meyer F, Mormann S, Munoz-Dorado J, Perez J, Pradella S, Rachid S, Raddatz G, Rosenau F, Ruckert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A, Velicer GJ, Vorholter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S, Wittmann C, Blocker H, Puhler A, Muller R., Nat. Biotechnol. 25(11), 2007
PMID: 17965706
Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L, Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T, Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy AC, Merai M, Meyer F, Mormann S, Munoz-Dorado J, Perez J, Pradella S, Rachid S, Raddatz G, Rosenau F, Ruckert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A, Velicer GJ, Vorholter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S, Wittmann C, Blocker H, Puhler A, Muller R., Nat. Biotechnol. 25(11), 2007
PMID: 17965706
Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis.
Schneiker S, Martins dos Santos VA, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Puhler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorholter FJ, Weidner S, Kaiser O, Golyshin PN., Nat. Biotechnol. 24(8), 2006
PMID: 16878126
Schneiker S, Martins dos Santos VA, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Puhler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorholter FJ, Weidner S, Kaiser O, Golyshin PN., Nat. Biotechnol. 24(8), 2006
PMID: 16878126
AUTHOR UNKNOWN, 0
The Staden package, 1998.
Staden R, Beal KF, Bonfield JK., Methods Mol. Biol. 132(), 2000
PMID: 10547834
Staden R, Beal KF, Bonfield JK., Methods Mol. Biol. 132(), 2000
PMID: 10547834
Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology.
Szczepanowski R, Bekel T, Goesmann A, Krause L, Kromeke H, Kaiser O, Eichler W, Puhler A, Schluter A., J. Biotechnol. 136(1-2), 2008
PMID: 18586057
Szczepanowski R, Bekel T, Goesmann A, Krause L, Kromeke H, Kaiser O, Eichler W, Puhler A, Schluter A., J. Biotechnol. 136(1-2), 2008
PMID: 18586057
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.
Tauch A, Kaiser O, Hain T, Goesmann A, Weisshaar B, Albersmeier A, Bekel T, Bischoff N, Brune I, Chakraborty T, Kalinowski J, Meyer F, Rupp O, Schneiker S, Viehoever P, Puhler A., J. Bacteriol. 187(13), 2005
PMID: 15968079
Tauch A, Kaiser O, Hain T, Goesmann A, Weisshaar B, Albersmeier A, Bekel T, Bischoff N, Brune I, Chakraborty T, Kalinowski J, Meyer F, Rupp O, Schneiker S, Viehoever P, Puhler A., J. Bacteriol. 187(13), 2005
PMID: 15968079
Ultrafast de novo sequencing of Corynebacterium urealyticum using the Genome Sequencer 20 System
Tauch, Biochemica 4(), 2006
Tauch, Biochemica 4(), 2006
The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing.
Tauch A, Trost E, Tilker A, Ludewig U, Schneiker S, Goesmann A, Arnold W, Bekel T, Brinkrolf K, Brune I, Gotker S, Kalinowski J, Kamp PB, Lobo FP, Viehoever P, Weisshaar B, Soriano F, Droge M, Puhler A., J. Biotechnol. 136(1-2), 2008
PMID: 18367281
Tauch A, Trost E, Tilker A, Ludewig U, Schneiker S, Goesmann A, Arnold W, Bekel T, Brinkrolf K, Brune I, Gotker S, Kalinowski J, Kamp PB, Lobo FP, Viehoever P, Weisshaar B, Soriano F, Droge M, Puhler A., J. Biotechnol. 136(1-2), 2008
PMID: 18367281
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence.
Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Buttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klosgen U, Patschkowski T, Ruckert C, Rupp O, Schneiker S, Schuster SC, Vorholter FJ, Weber E, Puhler A, Bonas U, Bartels D, Kaiser O., J. Bacteriol. 187(21), 2005
PMID: 16237009
Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Buttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klosgen U, Patschkowski T, Ruckert C, Rupp O, Schneiker S, Schuster SC, Vorholter FJ, Weber E, Puhler A, Bonas U, Bartels D, Kaiser O., J. Bacteriol. 187(21), 2005
PMID: 16237009
The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.
Vorholter FJ, Schneiker S, Goesmann A, Krause L, Bekel T, Kaiser O, Linke B, Patschkowski T, Ruckert C, Schmid J, Sidhu VK, Sieber V, Tauch A, Watt SA, Weisshaar B, Becker A, Niehaus K, Puhler A., J. Biotechnol. 134(1-2), 2008
PMID: 18304669
Vorholter FJ, Schneiker S, Goesmann A, Krause L, Bekel T, Kaiser O, Linke B, Patschkowski T, Ruckert C, Schmid J, Sidhu VK, Sieber V, Tauch A, Watt SA, Weisshaar B, Becker A, Niehaus K, Puhler A., J. Biotechnol. 134(1-2), 2008
PMID: 18304669
Transcriptional changes in response to arbuscular mycorrhiza development in the model plant Medicago truncatula.
Wulf A, Manthey K, Doll J, Perlick AM, Linke B, Bekel T, Meyer F, Franken P, Kuster H, Krajinski F., Mol. Plant Microbe Interact. 16(4), 2003
PMID: 12744459
Wulf A, Manthey K, Doll J, Perlick AM, Linke B, Bekel T, Meyer F, Franken P, Kuster H, Krajinski F., Mol. Plant Microbe Interact. 16(4), 2003
PMID: 12744459
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