RAPYD - Rapid Annotation Platform for Yeast Data
Schneider J, Blom J, Jaenicke S, Linke B, Brinkrolf K, Neuweger H, Tauch A, Goesmann A (2011)
Journal of Biotechnology 155(1): 118-126.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Einrichtung
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Arbeitsgruppe A. Tauch
Technische Fakultät > Computational Genomics
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Arbeitsgruppe A. Tauch
Technische Fakultät > Computational Genomics
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Centrum für Biotechnologie > Institut für Bioinformatik
Abstract / Bemerkung
Lower eukaryotes of the kingdom Fungi include a variety of biotechnologically important yeast species that are in the focus of genome research for more than a decade. Due to the rapid progress in ultra-fast sequencing technologies, the amount of available yeast genome data increases steadily. Thus, an efficient bioinformatics platform is required that covers genome assembly, eukaryotic gene prediction, genome annotation, comparative yeast genomics, and metabolic pathway reconstruction. Here, we present a bioinformatics platform for yeast genomics named RAPYD addressing the key requirements of extensive yeast sequence data analysis. The first step is a comprehensive regional and functional annotation of a yeast genome. A region prediction pipeline was implemented to obtain reliable and high-quality predictions of coding sequences and further genome features. Functions of coding sequences are automatically determined using a configurable prediction pipeline. Based on the resulting functional annotations, a metabolic pathway reconstruction module can be utilized to rapidly generate an overview of organism-specific features and metabolic blueprints. In a final analysis step shared and divergent features of closely related yeast strains can be explored using the comparative genomics module. An in-depth application example of the yeast Meyerozyma guilliermondii illustrates the functionality of RAPYD. A user-friendly web interface is available at https://rapyd.cebitec.uni-bielefeld.de. (C) 2010 Elsevier B. V. All rights reserved.
Stichworte
Yeasts;
Comparative genomics;
Meyerozyma guilliermondii;
Metabolic pathways;
Genome annotation
Erscheinungsjahr
2011
Zeitschriftentitel
Journal of Biotechnology
Band
155
Ausgabe
1
Seite(n)
118-126
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/2326445
Zitieren
Schneider J, Blom J, Jaenicke S, et al. RAPYD - Rapid Annotation Platform for Yeast Data. Journal of Biotechnology. 2011;155(1):118-126.
Schneider, J., Blom, J., Jaenicke, S., Linke, B., Brinkrolf, K., Neuweger, H., Tauch, A., et al. (2011). RAPYD - Rapid Annotation Platform for Yeast Data. Journal of Biotechnology, 155(1), 118-126. https://doi.org/10.1016/j.jbiotec.2010.10.076
Schneider, Jessica, Blom, Jochen, Jaenicke, Sebastian, Linke, Burkhard, Brinkrolf, Karina, Neuweger, Heiko, Tauch, Andreas, and Goesmann, Alexander. 2011. “RAPYD - Rapid Annotation Platform for Yeast Data”. Journal of Biotechnology 155 (1): 118-126.
Schneider, J., Blom, J., Jaenicke, S., Linke, B., Brinkrolf, K., Neuweger, H., Tauch, A., and Goesmann, A. (2011). RAPYD - Rapid Annotation Platform for Yeast Data. Journal of Biotechnology 155, 118-126.
Schneider, J., et al., 2011. RAPYD - Rapid Annotation Platform for Yeast Data. Journal of Biotechnology, 155(1), p 118-126.
J. Schneider, et al., “RAPYD - Rapid Annotation Platform for Yeast Data”, Journal of Biotechnology, vol. 155, 2011, pp. 118-126.
Schneider, J., Blom, J., Jaenicke, S., Linke, B., Brinkrolf, K., Neuweger, H., Tauch, A., Goesmann, A.: RAPYD - Rapid Annotation Platform for Yeast Data. Journal of Biotechnology. 155, 118-126 (2011).
Schneider, Jessica, Blom, Jochen, Jaenicke, Sebastian, Linke, Burkhard, Brinkrolf, Karina, Neuweger, Heiko, Tauch, Andreas, and Goesmann, Alexander. “RAPYD - Rapid Annotation Platform for Yeast Data”. Journal of Biotechnology 155.1 (2011): 118-126.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
9 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines.
Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Pühler A, Noll T, Goesmann A., PLoS One 9(1), 2014
PMID: 24427317
Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Pühler A, Noll T, Goesmann A., PLoS One 9(1), 2014
PMID: 24427317
Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.).
Becker J, Timmermann C, Rupp O, Albaum SP, Brinkrolf K, Goesmann A, Pühler A, Tauch A, Noll T., J Biotechnol 178(), 2014
PMID: 24613301
Becker J, Timmermann C, Rupp O, Albaum SP, Brinkrolf K, Goesmann A, Pühler A, Tauch A, Noll T., J Biotechnol 178(), 2014
PMID: 24613301
Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes.
Zhao XQ, Aizawa T, Schneider J, Wang C, Shen RF, Sunairi M., Microbiologyopen 2(2), 2013
PMID: 23427135
Zhao XQ, Aizawa T, Schneider J, Wang C, Shen RF, Sunairi M., Microbiologyopen 2(2), 2013
PMID: 23427135
Candida guilliermondii: biotechnological applications, perspectives for biological control, emerging clinical importance and recent advances in genetics.
Papon N, Savini V, Lanoue A, Simkin AJ, Crèche J, Giglioli-Guivarc'h N, Clastre M, Courdavault V, Sibirny AA., Curr Genet 59(3), 2013
PMID: 23616192
Papon N, Savini V, Lanoue A, Simkin AJ, Crèche J, Giglioli-Guivarc'h N, Clastre M, Courdavault V, Sibirny AA., Curr Genet 59(3), 2013
PMID: 23616192
Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1.
Ravin NV, Eldarov MA, Kadnikov VV, Beletsky AV, Schneider J, Mardanova ES, Smekalova EM, Zvereva MI, Dontsova OA, Mardanov AV, Skryabin KG., BMC Genomics 14(), 2013
PMID: 24279325
Ravin NV, Eldarov MA, Kadnikov VV, Beletsky AV, Schneider J, Mardanova ES, Smekalova EM, Zvereva MI, Dontsova OA, Mardanov AV, Skryabin KG., BMC Genomics 14(), 2013
PMID: 24279325
A systems-level approach for metabolic engineering of yeast cell factories.
Kim IK, Roldão A, Siewers V, Nielsen J., FEMS Yeast Res 12(2), 2012
PMID: 22188344
Kim IK, Roldão A, Siewers V, Nielsen J., FEMS Yeast Res 12(2), 2012
PMID: 22188344
Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities.
Schneider J, Rupp O, Trost E, Jaenicke S, Passoth V, Goesmann A, Tauch A, Brinkrolf K., FEMS Yeast Res 12(3), 2012
PMID: 22292503
Schneider J, Rupp O, Trost E, Jaenicke S, Passoth V, Goesmann A, Tauch A, Brinkrolf K., FEMS Yeast Res 12(3), 2012
PMID: 22292503
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach.
Proux-Wéra E, Armisén D, Byrne KP, Wolfe KH., BMC Bioinformatics 13(), 2012
PMID: 22984983
Proux-Wéra E, Armisén D, Byrne KP, Wolfe KH., BMC Bioinformatics 13(), 2012
PMID: 22984983
Draft genome sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10.
Schneider J, Andrea H, Blom J, Jaenicke S, Rückert C, Schorsch C, Szczepanowski R, Farwick M, Goesmann A, Pühler A, Schaffer S, Tauch A, Köhler T, Brinkrolf K., Eukaryot Cell 11(12), 2012
PMID: 23193139
Schneider J, Andrea H, Blom J, Jaenicke S, Rückert C, Schorsch C, Szczepanowski R, Farwick M, Goesmann A, Pühler A, Schaffer S, Tauch A, Köhler T, Brinkrolf K., Eukaryot Cell 11(12), 2012
PMID: 23193139
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Daten bereitgestellt von Europe PubMed Central.
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