Services: Software Tools

Interaction Network GO Annotator is a web server for the prediction of protein function.

Prediction of protein stability change upon single-point variations from protein sequence and structure

A web service for the structural annotation of protein-protein interaction networks. 

A database framework widely used to support model organism databases. 

iPath is a web-based tool for the visualization and analysis of cellular pathways. Based on current annotations (such as KEGG), it provides pathway maps for primary cellular metabolism as well as for some additional secondary metabolite synthesis and regulatory pathways. Users can map their own data onto these pathway maps. Due to its navigation and customization functions, iPATH thus allows users to easily explore and analyze the functional and metabolic capabilities of their (meta-)genomic data sets. Part of the Microbiome Analysis Toolbox. 

Non-coding genome sequences and genetic network tools. The IRESite presents experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions.

Models genome-wide expression data in terms of genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample- dependent activities, and their genome-wide targets. 

A means for determining the pattern occurring in groups of isogenic individual mutations (SNP, deletion, insertion)

Interactive Tree Of Life (iTOL) is an online tool for the display and manipulation of phylogenetic trees. It provides a large variety of tree layouts, drawing and annotation features including circular tree layout, which is well-suited particularly for mid-sized trees (up to several thousand leaves). Tree displays can be exported in several graphical formats, both bitmap and vector based. Part of the Microbiome Analysis Toolbox. 

Tool for determining disordered protein regions

Jalview is a Win/Mac/Linux/Web interactive graphical interface and command line tool for molecular sequence, alignment and 3D structure bioinformatics resource interoperability.

JAMDA docks small molecules into protein binding sites.

KEGGanim is a tool for visualizing data in the context of biological pathways. KEGGanim produces animations or static images of KEGG pathways by overlaying high-throughput data over handdrawn KEGG pathway maps.

This workflow reads images from a high throughput experiment acquired with an Olympus ScanR Microscope. A subset of the image data is used to train a classifier, which is then applied to the whole dataset. A classifier is trained on exemplary images and applied to the whole dataset.

Virtual infrastructure network supporting cooperation between research units 

Access to aRNA research tools for secondary structure prediction, structure alignments, interaction prediction, kinetics etc. Databases and Utils include:

• TRNAdb
• Mitos
• DARIO
• Plexy
• RNAsnoop
• RNAstrand 
• Ryoto

A web tool and a mobile app for exploring the entire Tree of Life

LifeSoaks calculates solvent channels and their corresponding bottleneck radii by constructing a three dimensional Voronoi diagram. 

Lipidomics Informatics for Life Sciences (LIFS) provides the bioinformatic framework to understand lipids in context and create an integrative systems biology view for lipid research.

Genomic analyses require flexible models that can be adapted to the needs of the user. Limix is a flexible and efficient linear mixed model library with interfaces to Python.

Provides access to lipid nomenclature, databases, tools, protocols, standards, tutorials, meetings, publications, and other resources and serving the international lipid research community.

LoRDEC is a standalone software for error correcting long reads (from Pacific Biosciences, or Oxford Nanopore) with a hybrid approach. LoRDEC uses short reads to correct long reads; it combines sequencing data from both the second and third generation technologies. It can be easily integrated in any pipeline for processing deep sequencing data. LoRDEC's originality is to build a graph that summarize all short reads, and then to align the long reads against this graph to correct them. This makes LoRDEC a very efficient tool to process large datasets. It has been widely used in whole genome or transcriptome projects around the world.

A java tool for profiling short-read sequences from T cell receptors and immunoglobulins

M-IOLITE is a computational suite for the efficient and automatic analysis of GC-MS metabolomic datasets integrating: (a) a standardized repository based on a standardized GC-MS peak library, (2) specialized GC-MS metabolomic data normalization, validation and filtering methods and (3) tool for unknown metabolite peak identification based on metabolic network analysis and visualization.

Methylation-Aware Genotype Association in R (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. 

A web application for the display and analysis of next-generation sequencing data with a focus on COVID-19 running on the de.NBI cloud infrastructure.

Multivariate Asymptotic Non-Parametric Test of Association

dSysMap (Mapping of Human disease-related mutations at the systemic level) displays Human disease-related mutations on the structural interactome. Mapping of mutations on protein structures and on interaction interfaces allows you to visualize the region of the interactome that they affect and helps in rationalizing their mechanism of action.

Freely accessible microbial genomics and metagenomics reference databases that include MarRef, MarDB, and MarCat. The MMP also includes a search engine that you can use to query all three databases at once.