Service list
Name of service | Description | Related links* |
---|---|---|
LoRDEC |
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. |
bio.tools |
LymAnalyzer |
A java tool for profiling short-read sequences from T cell receptors and immunoglobulins |
bio.tools |
M-IOLITE |
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. |
bio.tools |
Magellan |
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. |
|
manta/mvgwas-nf |
Multivariate Asymptotic Non-Parametric Test of Association |
bio.tools |
Mapping human disease-mutations at systemic level (dSysMap) |
Display of 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. |
bio.tools |
Mapping human disease-mutations at systemic level (dSysMap) |
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. |
bio.tools |
Marine Metagenomics Portal (MMP) |
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. |
bio.toolsTeSS |
MassBank |
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). |
FAIRsharing |
MasterOfPores |
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). |
bio.tools |
MATRIXDB |
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. |
FAIRsharing |
MCL |
Efficient graph clustering tool with a collection of use cases for protein family detection, orthology assignment and protein interaction module discovery (Emerging Service) |
|
Mechismo |
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. |
|
Medusa |
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. |
bio.tools |
MeltDB |
Analysis of raw GC- and LC-MS metabolome data against the either the GMD database or user defined libraries in NIST. |
bio.tools |
MEM |
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. |
bio.tools |
Mentha |
A comprehensive collection of data from manually curated protein-protein interaction databases adhering to the IMEx consortium. |
bio.toolsFAIRsharing |
Mercator |
Mercator is a web server that is able to assign functional terms to protein or nucleotide sequences. |
bio.tools |
MESBL GC-MS metabolite peak database |
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. |
bio.tools |
MÉTA Programme |
Website encompassing vegetation heritage data of Hungary, including |
|
META-pipe |
The META-pipe pipeline for annotation and analysis of marine metagenomics samples provides insight into phylogenetic diversity and metabolic and functional potential of environmental communities. |
bio.tools |
Metabolic Atlas |
Open-source infrastructure service for research and engineering of metabolism in model organisms and human |
bio.toolsFAIRsharing |
MetaboLights |
MetaboLights is a database for metabolomics experiments and derived information. |
bio.toolsFAIRsharingTeSS |
Metabolites Biological Role (MBROLE) |
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. |
bio.tools |
Metadyn View |
Interactive viewer of metadynamics results. |
bio.tools |
METAGEN |
METAGEN performs meta-analysis using fixed- and random-effects logistic regression models, treating the multiple genotypes as independent variables |
bio.tools |
MetaNetX |
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. |
bio.toolsFAIRsharing |
MetaPhOrs |
A public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in twelve public repositories. |
bio.tools |
MetaProSIP |
Automated inference of elemental fluxes in microbial communities, now integrated as TOPP into OpenMS |
|
metaseqR |
Analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms with optimized tradeoff between true and false hits. |
bio.tools |