Boas Pucker @ Rheinische Friedrich-Wilhelms-Universität Bonn
About
The department of Plant Biotechnology and Bioinformatics combines molecular biology of plant metabolism and computational methods to address questions around the evolution and regulation of biosynthesis pathways.
Services
Specific biological questions require the development of dedicated tools. We write such tools mostly in Python and R. The developed tools are freely available on GitHub (bpucker). Some tools are available on our web server. The following tools are examples of active developments.
KIPEs: Knowledge-based Identification of Pathway Enzymes allows the automatic annotation of the proteins involved in the core steps of the flavonoid biosynthesis. This supports the identification of molecular mechanisms underlying color differences between cultivars of the same species. In addition, rapid annotation of flavonoid biosynthesis genes in novel/uncharacterized species becomes convenient.
MGSE: Mapping-based Genome Size Estimation is a novel approach to infer the true genome size of a species based on sequence reads. This approach harnesses the equal representation of all regions (even repeats) in the read set. The average number of sequence reads (coverage) is estimated based on single copy regions in a reference genome sequence. Dividing the combined coverage of all positions in an assembly by this sequencing depth results in the genome size estimation.
NAVIP: Neighborhood-Aware Variant Impact Predictor enables the prediction of functional consequences arising from sequence variants between a sequenced sample and a reference. In contrast to many established tools, NAVIP considers all variants in one gene at the same time when predicting the potential effect of sequence variants.
MYB_annotator: This tool enables the automatic identification and annotation of MYBs in a novel transcriptome/genome sequence assembly of a plant species. The identified candidates are functionally annotated based on orthology to previously characterized sequences.
bHLH_annotator: This tool enables the automatic identification and annotation of bHLHs in a novel transcriptome/genome sequence assembly of a plant species. The identified candidates are functionally annotated based on orthology to previously characterized sequences.
Training activities will focus on 'Big Data Analytics for Life Scientists' and functional annotation of plant genome data.
Project Management
Rheinische Friedrich Wilhelms-Universität Bonn
Institut für Zelluäre und Molekulare Botanik
Pflanzenbiotechnologie und Bioinformatik
Kirschallee 1
53115 Bonn
Contact: