Service list

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.

The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes and much more.

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.

The Medical Proteome Center at Ruhr-University Bochum offer consulting and analysis services to support users in bioinformatics and statistical analysis of proteomics data and associated clinical data.

The Mass Centric Peptide Database contains the tryptic in silico digest of all known proteins in UniProt KB, stored in an efficient manner to be quickly searched.

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. 

The world's largest collection of cultivation media. The mission of MediaDive is to transform poorly structured media recipes into a standardized database.

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

A comprehensive collection of data from manually curated protein-protein interaction databases adhering to the IMEx consortium.

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

MESBL GC-MS metabolite peak database is a standardized library of more than 900 metabolite peaks from MS-reconstructed gas chromatograms integrating the in-house standard compound and peak library of the FORTH/ICE-HT Metabolic Engineering and Systems Biology Laboratory, appropriately filtered GOLM database peak information and Human Metabolome database information.

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

Open-source infrastructure service for research and engineering of metabolism in model organisms and human

MetaboLights is a database for metabolomics experiments and derived information.