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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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. 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.

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