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.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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.
Erscheinungsjahr
Zeitschriftentitel
Journal of Biotechnology
Band
155
Zeitschriftennummer
1
Seite
118-126
ISSN
PUB-ID

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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. doi:10.1016/j.jbiotec.2010.10.076
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.

9 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

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Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Pühler A, Noll T, Goesmann A., PLoS One 9(1), 2014
PMID: 24427317
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
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
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Kim IK, Roldão A, Siewers V, Nielsen J., FEMS Yeast Res 12(2), 2012
PMID: 22188344
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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
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

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