Services

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.

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).

Parallel and scalable workflow for the analysis of Oxford Nanopore direct RNA sequencing datasets. Nextflow pipeline for analysis of Nanopore reads (from RNA/cDNA/DNA).

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.

MeDeCom is an R package for reference-free decomposition of heterogeneous DNA methylation profiles. 

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.

A method for estimating disordered stretches in transmembrane proteins

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

An online platform for pooling the results of research with the same objectives

Server that performs functional enrichment analysis of a list of chemical compounds derived from a metabolomics experiment, which allows this list to be interpreted in biological terms.

Interactive viewer of metadynamics results.

METAGEN performs meta-analysis using fixed- and random-effects logistic regression models, treating the multiple genotypes as independent variables

METALizer predicts the coordination geometry of metals in metalloproteins.

MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular compartments - namely MNXref - and proteins. The MetaNetX.org website (http://www.metanetx.org/) provides access to these integrated data as well as a variety of tools that allow users to import their own GSMNs, map them to the MNXref reconciliation, and manipulate, compare, analyze, simulate (using flux balance analysis) and export the resulting GSMNs. MNXref and MetaNetX are regularly updated and freely available.

Automated inference of elemental fluxes in microbial communities, now integrated as TOPP into OpenMS

MetaProteomeAnalyzer is an intuitive open-source tool for metaproteomics data analysis and interpretation, which includes multiple search engines and the ability to decrease data redundancy by grouping protein hits into so-called metaproteins. 

Analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms with optimized tradeoff between true and false hits.

MetExplore is a free and open webserver for the analysis of omics data in the context of genome scale metabolic networks. MetExplore allows the collaborative curation of metabolic networks. In the specific case of metabolomics, it provides mining algorithms such as MetaboRank, a recommendation system for enhanced metabolic fingerprinting. Overall, Metexplore orginality relies in its ability to allow taylor made metabolic network visualisation using an open source javascript library: MetExploreViz.

MetFrag is a system for the annotation of tandem mass spectra of metabolites, performing in silico fragmentation and scoring.

methview.qc allows you to generate quality control plots from your methylation array dataset.

Providing a large infrastructure for the analysis and interpretation of metagenomics data