BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser
Goesmann A, Linke B, Bartels D, Dondrup M, Krause L, Neuweger H, Oehm S, Paczian T, Wilke A, Meyer F (2005)
Nucleic Acids Research 33(Web Server): W710-W716.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Goesmann, AlexanderUniBi 
;
Linke, BurkhardUniBi;
Bartels, Daniela;
Dondrup, Michael;
Krause, Lutz;
Neuweger, HeikoUniBi;
Oehm, SebastianUniBi;
Paczian, Tobias;
Wilke, Andreas;
Meyer, Folker
;
Linke, BurkhardUniBi;
Bartels, Daniela;
Dondrup, Michael;
Krause, Lutz;
Neuweger, HeikoUniBi;
Oehm, SebastianUniBi;
Paczian, Tobias;
Wilke, Andreas;
Meyer, FolkerEinrichtung
Abstract / Bemerkung
The growing amount of information resulting from the increasing number of publicly available genomes and experimental results thereof necessitates the development of comprehensive systems for data processing and analysis. In this paper, we describe the current state and latest developments of our BRIGEP bioinformatics software system consisting of three web-based applications: GenDB, EMMA and ProDB. These applications facilitate the processing and analysis of bacterial genome, transcriptome and proteome data and are actively used by numerous international groups. We are currently in the process of extensively interconnecting these applications. BRIGEP was developed in the Bioinformatics Resource Facility of the Center for Biotechnology at Bielefeld University and is freely available. A demo project with sample data and access to all three tools is available at https://www.cebitec.uni-bielefeld.de/groups/brf/software/brigep/. Code bundles for these and other tools developed in our group are accessible on our FTP server at ftp.cebitec.uni-bielefeld.de/pub/software/.
Erscheinungsjahr
2005
Zeitschriftentitel
Nucleic Acids Research
Band
33
Ausgabe
Web Server
Seite(n)
W710-W716
ISSN
0305-1048
eISSN
1362-4962
Page URI
https://pub.uni-bielefeld.de/record/1773644
Zitieren
Goesmann A, Linke B, Bartels D, et al. BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser. Nucleic Acids Research. 2005;33(Web Server):W710-W716.
Goesmann, A., Linke, B., Bartels, D., Dondrup, M., Krause, L., Neuweger, H., Oehm, S., et al. (2005). BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser. Nucleic Acids Research, 33(Web Server), W710-W716. https://doi.org/10.1093/nar/gki400
Goesmann, Alexander, Linke, Burkhard, Bartels, Daniela, Dondrup, Michael, Krause, Lutz, Neuweger, Heiko, Oehm, Sebastian, Paczian, Tobias, Wilke, Andreas, and Meyer, Folker. 2005. “BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser”. Nucleic Acids Research 33 (Web Server): W710-W716.
Goesmann, A., Linke, B., Bartels, D., Dondrup, M., Krause, L., Neuweger, H., Oehm, S., Paczian, T., Wilke, A., and Meyer, F. (2005). BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser. Nucleic Acids Research 33, W710-W716.
Goesmann, A., et al., 2005. BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser. Nucleic Acids Research, 33(Web Server), p W710-W716.
A. Goesmann, et al., “BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser”, Nucleic Acids Research, vol. 33, 2005, pp. W710-W716.
Goesmann, A., Linke, B., Bartels, D., Dondrup, M., Krause, L., Neuweger, H., Oehm, S., Paczian, T., Wilke, A., Meyer, F.: BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser. Nucleic Acids Research. 33, W710-W716 (2005).
Goesmann, Alexander, Linke, Burkhard, Bartels, Daniela, Dondrup, Michael, Krause, Lutz, Neuweger, Heiko, Oehm, Sebastian, Paczian, Tobias, Wilke, Andreas, and Meyer, Folker. “BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser”. Nucleic Acids Research 33.Web Server (2005): W710-W716.
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2019-09-06T08:48:08Z
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13 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Extracting biomarkers of commitment to cancer development: potential role of vibrational spectroscopy in systems biology.
Theophilou G, Paraskevaidi M, Lima KM, Kyrgiou M, Martin-Hirsch PL, Martin FL., Expert Rev Mol Diagn 15(5), 2015
PMID: 25804575
Theophilou G, Paraskevaidi M, Lima KM, Kyrgiou M, Martin-Hirsch PL, Martin FL., Expert Rev Mol Diagn 15(5), 2015
PMID: 25804575
afterParty: turning raw transcriptomes into permanent resources.
Jones M, Blaxter M., BMC Bioinformatics 14(), 2013
PMID: 24093729
Jones M, Blaxter M., BMC Bioinformatics 14(), 2013
PMID: 24093729
Deep sequencing of naupliar-, cyprid- and adult-specific normalised Expressed Sequence Tag (EST) libraries of the acorn barnacle Balanus amphitrite.
De Gregoris TB, Rupp O, Klages S, Knaust F, Bekel T, Kube M, Burgess JG, Arnone MI, Goesmann A, Reinhardt R, Clare AS., Biofouling 27(4), 2011
PMID: 21526438
De Gregoris TB, Rupp O, Klages S, Knaust F, Bekel T, Kube M, Burgess JG, Arnone MI, Goesmann A, Reinhardt R, Clare AS., Biofouling 27(4), 2011
PMID: 21526438
A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data.
Becker A, Barnett MJ, Capela D, Dondrup M, Kamp PB, Krol E, Linke B, Rüberg S, Runte K, Schroeder BK, Weidner S, Yurgel SN, Batut J, Long SR, Pühler A, Goesmann A., J Biotechnol 140(1-2), 2009
PMID: 19103235
Becker A, Barnett MJ, Capela D, Dondrup M, Kamp PB, Krol E, Linke B, Rüberg S, Runte K, Schroeder BK, Weidner S, Yurgel SN, Batut J, Long SR, Pühler A, Goesmann A., J Biotechnol 140(1-2), 2009
PMID: 19103235
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Dondrup M, Albaum SP, Griebel T, Henckel K, Jünemann S, Kahlke T, Kleindt CK, Küster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Pühler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358
Dondrup M, Albaum SP, Griebel T, Henckel K, Jünemann S, Kahlke T, Kleindt CK, Küster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Pühler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358
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, Goesmann A., J Biotechnol 140(1-2), 2009
PMID: 19297685
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., J Biotechnol 140(1-2), 2009
PMID: 19297685
Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies.
Bacchetti De Gregoris T, Borra M, Biffali E, Bekel T, Burgess JG, Kirby RR, Clare AS., BMC Mol Biol 10(), 2009
PMID: 19552808
Bacchetti De Gregoris T, Borra M, Biffali E, Bekel T, Burgess JG, Kirby RR, Clare AS., BMC Mol Biol 10(), 2009
PMID: 19552808
Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example.
Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Hüser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A., BMC Syst Biol 3(), 2009
PMID: 19698148
Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Hüser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A., BMC Syst Biol 3(), 2009
PMID: 19698148
MeltDB: a software platform for the analysis and integration of metabolomics experiment data.
Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A., Bioinformatics 24(23), 2008
PMID: 18765459
Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A., Bioinformatics 24(23), 2008
PMID: 18765459
CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks.
Baumbach J., BMC Bioinformatics 8(), 2007
PMID: 17986320
Baumbach J., BMC Bioinformatics 8(), 2007
PMID: 17986320
Mass spectrometric identification of proteins in complex post-genomic projects. Soluble proteins of the metabolically versatile, denitrifying 'Aromatoleum' sp. strain EbN1.
Hufnagel P, Rabus R., J Mol Microbiol Biotechnol 11(1-2), 2006
PMID: 16825790
Hufnagel P, Rabus R., J Mol Microbiol Biotechnol 11(1-2), 2006
PMID: 16825790
MannDB - a microbial database of automated protein sequence analyses and evidence integration for protein characterization.
Zhou CL, Lam MW, Smith JR, Zemla AT, Dyer MD, Kuczmarski TA, Vitalis EA, Slezak TR., BMC Bioinformatics 7(), 2006
PMID: 17044936
Zhou CL, Lam MW, Smith JR, Zemla AT, Dyer MD, Kuczmarski TA, Vitalis EA, Slezak TR., BMC Bioinformatics 7(), 2006
PMID: 17044936
26 References
Daten bereitgestellt von Europe PubMed Central.
Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.
Bernal A, Ear U, Kyrpides N., Nucleic Acids Res. 29(1), 2001
PMID: 11125068
Bernal A, Ear U, Kyrpides N., Nucleic Acids Res. 29(1), 2001
PMID: 11125068
Artemis: sequence visualisation and annotation
Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.-A., Barrell B.., 2000
Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.-A., Barrell B.., 2000
The ERGO genome analysis and discovery system.
Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E Jr, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P, Kapatral V, Mikhailova N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N., Nucleic Acids Res. 31(1), 2003
PMID: 12519973
Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E Jr, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P, Kapatral V, Mikhailova N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N., Nucleic Acids Res. 31(1), 2003
PMID: 12519973
BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data
Saal L.H., Troein C., Vallon-Christersson J., Gruvberger S., Saal L.H., Troein C., Vallon-Christersson J., Gruvberger S., Borg A., Peterson C.., 2002
Saal L.H., Troein C., Vallon-Christersson J., Gruvberger S., Saal L.H., Troein C., Vallon-Christersson J., Gruvberger S., Borg A., Peterson C.., 2002
GECKO: a complete large-scale gene expression analysis platform.
Theilhaber J, Ulyanov A, Malanthara A, Cole J, Xu D, Nahf R, Heuer M, Brockel C, Bushnell S., BMC Bioinformatics 5(), 2004
PMID: 15588317
Theilhaber J, Ulyanov A, Malanthara A, Cole J, Xu D, Nahf R, Heuer M, Brockel C, Bushnell S., BMC Bioinformatics 5(), 2004
PMID: 15588317
EMMA: a platform for consistent storage and efficient analysis of microarray data.
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651856
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651856
Bioinformatics support for high-throughput proteomics.
Wilke A, Ruckert C, Bartels D, Dondrup M, Goesmann A, Huser AT, Kespohl S, Linke B, Mahne M, McHardy A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651857
Wilke A, Ruckert C, Bartels D, Dondrup M, Goesmann A, Huser AT, Kespohl S, Linke B, Mahne M, McHardy A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651857
PRIME: a graphical interface for integrating genomic/proteomic databases.
Facius A, Englbrecht C, Birzele F, Groscurth A, Benjamin S, Wanka S, Mewes W., Proteomics 5(1), 2005
PMID: 15744835
Facius A, Englbrecht C, Birzele F, Groscurth A, Benjamin S, Wanka S, Mewes W., Proteomics 5(1), 2005
PMID: 15744835
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
Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology.
Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651858
Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651858
O2DBI II: ein Persistenzlayer für Perl-Objekte
Linke B.., 2002
Linke B.., 2002
Improved microbial gene identification with GLIMMER.
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL., Nucleic Acids Res. 27(23), 1999
PMID: 10556321
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL., Nucleic Acids Res. 27(23), 1999
PMID: 10556321
CRITICA: coding region identification tool invoking comparative analysis.
Badger JH, Olsen GJ, Woese CR., Mol. Biol. Evol. 16(4), 1999
PMID: 10331277
Badger JH, Olsen GJ, Woese CR., Mol. Biol. Evol. 16(4), 1999
PMID: 10331277
Development of joint application strategies for two microbial gene finders.
McHardy AC, Goesmann A, Puhler A, Meyer F., Bioinformatics 20(10), 2004
PMID: 14988122
McHardy AC, Goesmann A, Puhler A, Meyer F., Bioinformatics 20(10), 2004
PMID: 14988122
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM., Nucleic Acids Res. 29(1), 2001
PMID: 11125043
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM., Nucleic Acids Res. 29(1), 2001
PMID: 11125043
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
KEGG: kyoto encyclopedia of genes and genomes.
Kanehisa M, Goto S., Nucleic Acids Res. 28(1), 2000
PMID: 10592173
Kanehisa M, Goto S., Nucleic Acids Res. 28(1), 2000
PMID: 10592173
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV., Nucleic Acids Res. 29(1), 2001
PMID: 11125040
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV., Nucleic Acids Res. 29(1), 2001
PMID: 11125040
Design and implementation of microarray gene expression markup language (MAGE-ML)
Spellman P.T., Miller M., Stewart J., Troup C., Sarkans U., Chervitz S., Bernhart D., Sherlock G., Ball C., Lepage M.., 2002
Spellman P.T., Miller M., Stewart J., Troup C., Sarkans U., Chervitz S., Bernhart D., Sherlock G., Ball C., Lepage M.., 2002
The proteomics standards initiative.
Orchard S, Hermjakob H, Apweiler R., Proteomics 3(7), 2003
PMID: 12872238
Orchard S, Hermjakob H, Apweiler R., Proteomics 3(7), 2003
PMID: 12872238
Probability-based protein identification by searching sequence databases using mass spectrometry data.
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS., Electrophoresis 20(18), 1999
PMID: 10612281
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS., Electrophoresis 20(18), 1999
PMID: 10612281
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
Eng J.K., McCormack A.L., Yates J.R.., 1994
Eng J.K., McCormack A.L., Yates J.R.., 1994
EMBOSS: the European Molecular Biology Open Software Suite.
Rice P, Longden I, Bleasby A., Trends Genet. 16(6), 2000
PMID: 10827456
Rice P, Longden I, Bleasby A., Trends Genet. 16(6), 2000
PMID: 10827456
The composite genome of the legume symbiont
Galibert F., Finan T., Long S., Pühler A., Abola P., Ampe F., Barloy-Hubler F., Barnett M., Becker A., Boistard P.., 2001
Galibert F., Finan T., Long S., Pühler A., Abola P., Ampe F., Barloy-Hubler F., Barnett M., Becker A., Boistard P.., 2001
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