Databases and Resources
Software tools, resources and databases developed by bioinformaticians of the institute.
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.
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.
Automated and standardized data analysis tool for proteomic datasets (LC-MS/MS) including statistical analysis.
The Golm Metabolome Database (GMD) provides access to GC/MS mass spectral libraries, metabolite compound information, and annotation tools and services.
The Gene Co-expression Analysis Tool-box (GeneCAT) is a suite of microarray co-expression analysis tools for plant biology. The platform includes both standard co-expression tools such as gene clustering and expression profiling, as well as tools that combine co-expression analysis with BLAST for functional inferencing. Arabidopsis thaliana, Barley, Medicago and rice are featured plants.
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.
MapMan is a user-driven cross-platform application that displays large datasets (e.g. microarray-, proteomics-, enzyme- or RNA-Seq data) on diagrams of metabolic pathways or other processes. This allows the user to visually explore the data in it's biological context which helps gaining deeper insights into the analysed experiment.MapMan also provides further modules that anable to explore the data from different "angles": Clustering of co-responding features, PageMan analysis of differential pathway regulation, Venn diagrams etc. thereby providing a versatile tool box for "omics" experiment analysis.
Unified classification structure for genes from different organisms for use in the MapMan tool.
Matapax is a web-based platform that incorporates recent Arabidopsis thaliana genotyping efforts, seeks to provide support for quick and easy association studies and is suitable for researchers without a strong statistical background. Computational time is reduced by processing user-supplied trait data in parallel. Result analysis is facilitated by displaying annotated candidate markers in tabular format and in a genome browser. Importantly, to assist collaboration and publication efforts, users can allow other users or reviewers access their data. Matapax can also be extended to incorporate other plant species.
Using the Mercator web application you can assign MapMan "Bins" to arbitrary DNA or protein input sequences.
The output will be a text file mapping each input identifier to one or more Bins. This file can directly be used as a mapping file for the high-throughput data visualization and meta-analysis software MapMan.
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).
MIRMYC is a miRNA and miRNA target database of mycorrhizal and non-mycorrhizal Medicago truncatula roots
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.
Short description: Database of plant protein phosphorylation sites, phosphorylation site predictor, kinase target search
Long description: PhosPhAt is a database hosting information of protein phosphorylation sites determined from large-scale phosphoproteomic experiments in plants, mainly Arabidopsis. In addition, PhosPhAt also inclueds a plant-specific phosphorylation site predictor for pS, pT and pY sites. Access to prediction algorithm now allows "on-the-fly" prediction of phosphorylation of any user uploaded protein sequence. Protein Pfam domain structures as well as phosphorylation site hotspots are mapped onto the protein sequence display besides to experimental and predicted phosphorylation sites. New developments incude searchable information of plant protein kinase targets.
The model organism Arabidopsis thaliana is readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer acquired knowledge from Arabidopsis to crop species. However, the identification of functional equivalents of well-characterized Arabidopsis genes in other plants is a nontrivial task. It is well documented that transcriptionally coordinated genes tend to be functionally related and that such relationships may be conserved across different species and even kingdoms. To exploit such relationships, we constructed whole-genome coexpression networks for Arabidopsis and six important plant crop species. The interactive networks, clustered using the HCCA algorithm, are provided under the banner PlaNet (http://aranet.mpimp-golm.mpg.de). We implemented a comparative network algorithm that estimates similarities between network structures. Thus, the platform can be used to swiftly infer similar coexpressed network vicinities within and across species and can predict the identity of functional homologs. We exemplify this using the PSA-D and chalcone synthase-related gene networks. Finally, we assessed how ontology terms are transcriptionally connected in the seven species and provide the corresponding MapMan term coexpression networks. The data support the contention that this platform will considerably improve transfer of knowledge generated in Arabidopsis to valuable crop species. PlaNet was developed by Marek Mutwil.
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.
RNA Loop Modeling based on homology and geometric constraints and RNA Loop Database.
RobiNA is a user-friendly cross-platform java application enabling users
to quality check and analyse differential expression analysis experiments based
on RNA-Seq and microarray data. It is tightly linked with the visualization
and pathway analysis software MapMan.
SATlotyper is a software tool designed for inferring haplotypes from polyploid and polyallelic unphased SNP data.
TagFinder for the quantitative analysis of gas chromatography - mass spectrometry (GC-MS) based metabolite profiling experiments
TagFinder performs a non-biased, multi-parallel analysis of GC-EI-TOF-MS metabolite profiles starting from chromatogram files and ending with a data matrix. This resulting data matrix can be used for the non-biased search for metabolic markers and metabolite identification within complex profiling experiments.
If you have any questions about TagFinder, please contact Alexander Erban
XEML Lab has been created to assist plant biologists in designing and documenting simple or sophisticated experiments in a machine readable format, to link this metadata with any type of data generated in the corresponding experiments, and ultimately, to make both metadata and data available for data mining.
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.
A TagFinder based high throughput tool for the mass isotope correction of GC-MS flux profiling experiments.
Download the CORRECTOR software here:
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Design 2 Color MicroArrays contains a few R-scripts, mainly the function optimize.MA.design which builds upon the daMA package.
Documentation system for plant transformation service and research
Database system to document standard operation procedures and experiments. Blank database available.
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.
A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research.
Mycproteom is a database representing cell specific proteome alterations of mycorrhizal M. truncatula roots.
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.