Welcome

This web server provides online access to a series of tools developed by the Freiburg Bioinformatics Group. To start using it, please select from the listings below, or use the menu on the left. If you prefer doing a local installation on your machine, please visit our 'Download' section.

If you use our tools for research or education, please cite the corresponding articles from the 'Publications' section.

Version 5.0.10

MoDPepInt Server

MoDPepInt (Modular Domain Peptide Interaction) is a simple and interactive webserver, which comprises three different tools, i.e. SH2PepInt, SH3PepInt and PDZPepInt, for predicting the binding partners of three different modular protein domains, i.e. SH2, SH3 and PDZ domains, respectively.

SH2PepInt

SH2PepInt has been developed to predict binding partners to more than 50 human SH2 domains. Depending on the user requirement it uses PhosphoSitePlus and Gene Ontology databases for predicting highly reliable SH2-peptide interactions.

SH3PepInt

SH3PepInt is a fast and sophisticated graph kernel based tool to predict SH3-peptide interactions. About 70 built-in models are available for SH3-peptide predictions. It does not need any pre-alignment of the peptides and uses Gene Ontology database for getting more reliable interactions.

PDZPepInt

PDZPepInt is a cluster based prediction tool to predict binding peptides of PDZ domains in human, mouse, fly and worm. About 40 built-in models that cover more than 220 PDZ domains across the species are available. Gene Ontology database can be used for getting reliable interactions. Additionally, it will also consider the C-terminal peptides that are intrinsically unstructured for getting high confidence interactions.

MetaServer

MoDPepInt is a meta-tool that runs interaction screens for all domains-specific tools listed here. It might be used as a starting point if no target domain information is known.

The Freiburg Bioinformatics Group also provides:

Freiburg RNA Tools

RNA Tools

Freiburg RNA tools provides online access to a series of RNA research tools developed by the Freiburg Bioinformatics Group and colleagues for sequence-structure alignments (LocARNA, CARNA, MARNA), clustering (ExpaRNA), interaction prediction (IntaRNA, CopraRNA, metaMIR), identification of homologs (GLASSgo), sequence design (AntaRNA, INFORNA, SECISDesign), CRISPR repeat analyses (CRISPRmap), and many more tasks.

CPSP-Tools Server

CPSP

CPSP (Constraint-based Protein Structure Prediction) is an exact and efficient approach to identify optimal structures of lattice proteins within the hydrophobic-polar (HP) model. The approach enables structure prediction within the 3D cubic and 3D face-centered-cubic (FCC) lattice for both backbone-only as well as side-chain representing models.

Galaxy Project - Uni Freiburg

Galaxy-FR

The Freiburg Galaxy Team offers a framework for scientists on e.g. NGS data analyses (RNA-seq, ChIP-seq, Exome-seq, MethylC-seq), genome annotation analyses for eukaryotic and prokaryotic organisms (from gene prediction to functional description), Proteomics and Metabolomics analysis, and the ChemicalToolBoX for analysis of small compounds. Galaxy contains more than 800 different single analysis tools and ready-to-use pipelines for different applications.

The Freiburg Galaxy Project is part of the “German Network for Bioinformatics Infrastructure” (Deutsches Netzwerk für Bioinformatik-Infrastruktur, de.NBI) and the Collaborative Research Centre (CRC) 992 for Medical Epigenetics and offers within the RNA Bioinformatic Centre (RBC) a central platform for RNA analysis.

CMV server

CMV (co-variance model visualization) offers tools for the visualization of RNA family models, also known as co-variance models (CM) and Hidden Markov Models (HMM). Moreover, comparisons between models, the multiple sequence alignments they were constructed from and, in the case of RNA families, the consensus secondary structure can be visualized. The aim is to simplify model construction and evaluation by providing visualizations with different levels of detail.

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MoDPepInt Server