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Tools & Services

Methods, tool, databases etc. developed by members of the group


This toolkit allows the assembly of up to 25 transcriptional units, consisting of many more individual DNA fragments, on a single plasmid in the host Saccharomyces cerevisiae. The assembly strategy employs recombination-based cloning methods. These methods allow a highly flexible assembly of different DNA parts, independent of restriction sites, thereby avoiding scar sequences. Furthermore, subcloning of the multi-gene assembly product into other destination vectors for gene expression in virtually any organism is straightforward. The web tool helps you planning the assembly.

BioNet Reasoning
Command line application for modeling biological systems. It allows to reason, i.e. predict, explain, and plan, about biological systems that are described in the action language C_TAID.

Clustering using a priori information via unsupervised decision trees is a method for extracting groups of samples in a microarray experiment. The result is directly interpretable as the method uses pre-defined classes of genes (such as those from Gene ontology or MapMan) to build a clustering tree with the informative gene classes as its nodes and groups of samples as its leaves.

CERMT (Covariance-based Extraction of Regulatory targets using Multiple Time series) is a method for predicting transcription factor targets given a particular transcription factor of interest. Targets are defined as the genes that responds similarly, but possibly time shifted, to the transcription factor under two or more treatments.

ChlamyCyc is an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. It provides extensive metabolic pathway information including comparative analysis, a genome browser, gene and protein-related sequence data, a Blast server for sequence search and alignments against various databases, annotation of proteins to MapMan BINs, domain information, peptide covering, ESTs, RNAs and their mapping onto genomic sequence, orthology relationships, and links to external Chlamydomonas-related resources.

GabiPD (The GABI Primary Database) is a web-accessible database established in the frame of the German initiative GABI (Genome Analysis of the Plant Biological System) to integrate, analyze and visualize primary data generated in GABI projects. Plant data from different ‘omics’ fronts representing more than 10 different model or crop species are integrated in GabiPD.

The Golm Metabolome Database (GMD) provides access to GC/MS mass spectral libraries, metabolite compound information, and annotation tools and services.

GraPPLE is a computational method for predicting functional non-coding RNA and classifying them to RNA families. The method relies on describing RNA structures as graphs, and introduces the use of associated graph properties as features in Support Vector Machines for prediction purposes.

Unified classification structure for genes from different organisms for use in the MapMan tool. (under development)

Matapax is an online platform designed to make association studies easier to perform for key organisms. Simply upload the trait measurements and Matapax will do the rest. Currently, Matapax can be used to perform association analyses on Arabidopsis thaliana and certain human cell lines.

web-based tool for the visualization and analysis of large-scale transcript and metabolite profile datasets. Standard methods (PCA, clustering) are provided as well as state-of-the-art methods such as independent component analysis (ICA).

OGDraw (OrganelleGenomeDraw) is a tool that enables the user to quickly generate high-quality graphical maps of circular DNA sequences. Though especially designed and optimized for the display of small organelle genomes like the chloroplast or mitochondrial genome, it is applicable to all circular DNA sequences. The input data can be provided as GenBank files or GenBank accession numbers.

Pathway Visualization and Editing System. Allows user-driven, interactive creation and visualization of pathway maps.

Data management pipeline for plant phenotyping in a multisite project. The website provides standardized data storage for meaningful data evaluation and statistical analysis.

Phos3D is a web server for the prediction of phosphorylation sites (P-sites) in proteins. The approach is based on Support Vector Machines trained on sequence profiles enhanced by information from the spatial context of experimentally identified P-sites.

the tool PROfile analysis based on Mutual Information (PROMI) enables comparative protein sequence analysis in terms of group-specific conservation. Positions in user-defined protein sequence motifs are identified that exhibit group-specific (e.g. species-specific) conservation and,thus, allows the elucidation of evolutionary characteristics.

QuantPrime is an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale real-time reverse transcription qPCR (also known as realtime qRT-PCR or RT-qPCR) analyses.

Robin (the helper of MapMan) is a user friendly graphical interface for powerful microarray data processing.

SATlotyper is a software tool designed for inferring haplotypes from polyploid and polyallelic unphased SNP data.

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