Services: software tools

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

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.

A meta-analysis-based tool for estimating tumor biomarkers

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.

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

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.

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.

A web tool for the integrative analysis of in silico miRNA target predictions, and reconstruction of post-transcriptional and mixed regulatory networks. 

(Service no longer available?) 

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.

Development of the software plattform for MassBank, a database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da).

MatrixDB is a database focused on molecular interactions of extracellular matrix proteins and glycosaminoglycans. The advanced query interface allows users to browse MatrixDB data, to build and to visualize specific interaction networks based on transcriptomic or quantitative proteomic data, diseases, biological processes or molecular functions. MatrixDB hosts the GAG builder tool to build on line 3D models of GAG sequences binding to proteins. 

Efficient graph clustering tool with a collection of use cases for protein family detection, orthology assignment and protein interaction module discovery (Emerging Service) 

Mechismo is a tool that allows rapid predictions of how genetic variants impact on biomolecular function. This is done by a pre-computed collection of protein-protein, protein-DNA/RNA, protein-chemical interactions of known three-dimensional structure mapped to proteomes from major model organisms. Users can input any number of variants to get a ranked list of genes and specific positions that have a functional impact on biomolecular interactions.

A tool for genome scaffolding that exploits information obtained from a set of (draft or closed) genomes to determine the correct order and orientation of the contigs.

Analysis of raw GC- and LC-MS metabolome data against the either the GMD database or user defined libraries in NIST.

MEM is a web-based multi experiment gene expression query and visualization tool. It gathers thousands of publicly available gene expression data sets from ArrayExpress database.

Mercator is a web server that is able to assign functional terms to protein or nucleotide sequences.