Services: software tools

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.

Interactive viewer of metadynamics results.

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

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

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.

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

OpenMS workflow for identification and quantification of HLA ligands.

A software pipeline for the processing of amplicon sequencing data, from raw sequences to OTU tables, taxonomy classification and phylogenetic tree inference

Micro-tomography (micro-computed tomography or microCT) is a method of non-destructive 3D x-ray microscopy, which allows the users to create 3D models of objects from a series of x-ray projection images, similar to the conventional clinical computer tomography. The MicroCT Service offers a collection of virtual galleries of taxa which will be displayed and disseminated through a web-based framework, and allows the user to manipulate the 3D models through a series of online tools or to download the datasets for local manipulations.

A compilation of tools offering identification and quantification of microorganisms, working with cellular pathways, phylogenetic trees and microbial communities, including: 

• MOCAT - a modular and scalable software pipeline for analyzing shotgun metagenomics datasets generated with Illumina technology. 
• mOTUs - Metagenomic operational taxonomic units (mOTUs) allow for the quantification of known (sequenced) and unknown microorganisms at species-level resolution from shotgun sequencing data. 
• SIAMCAT -  a modular framework for the statistical inference of associations between microbial communities and host phenotypes, such as disease states in clinical case-control studies. 
• eggNOG - a database of nested orthologous gene groups (NOGs) infered using unsupervised clustering applied to >2,000 complete genomes followed by comprehensive characterization and analysis of the resulting gene families. 
• Enterotyping - uses computational methods to detect and characterise densely populated regions in a high-dimensional space of microbiome community composition, by which human individuals can be stratified. 
• iPATH - 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. 
• iTOL - Interactive Tree Of Life (iTOL) is an online tool for the display and manipulation of phylogenetic trees. 

MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts.

microTSS is a machine-learning algorithm that provides highly accurate, single-nucleotide resolution predictions for intergenic miRNA transcription start sites (TSSs)

The Missense3D portal hosts resources developed to characterise and prioritise missense variants (amino acid substitutions) using protein three-dimensional structural information from models or experimental coordinates. Missense3D predicts the structural changes introduced by an amino acid substitution.

MobiDB-lite is an optimized method for highly specific predictions of long intrinsically disordered regions.

Intuitively, MOFA can be viewed as a versatile and statistically rigorous generalization of principal component analysis (PCA) to multi-omics data. Given several data matrices with measurements of multiple ‘omics data types on the same or on overlapping sets of samples, MOFA infers an interpretable low-dimensional data representation in terms of (hidden) factors. These learnt factors represent the driving sources of variation across data modalities, thus facilitating the identification of cellular states or disease subgroups.

MolArt (MOLeculAR structure annoTator) - molecular structure annotation and visualization tool.

Toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in (bio)macromolecular structures, e.g., proteins, RNA, DNA and biomacromolecular assemblies. 

Web interface providing a direct access to MOLE 2.0 functionality and enabling on-line and easy-to-use interactive channel analysis. 

MolMeDB is an open chemistry database about interactions of molecules with membranes.

Mol* is a web application for visualization of biomacromolecular structures including experimental data (for example electron densities) and annotations. Can visualize also molecular dynamics.

Web based application to validate ligand structure in PDB.

Metagenomic operational taxonomic units (mOTUs) allow for the quantification of known (sequenced) and unknown microorganisms at species-level resolution from shotgun sequencing data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to profile their abundances in shotgun metagenomic samples. Part of the Microbiome Analysis Toolbox. 

Tool to predict peptide fragment ion intensities for mass spectrometry-based proteomics data.

A highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from NGS data. Predicts mitochondrial haplogroups.

A tool for analyzing PCR primer compatibility and automatically finding optimal multiplexing (grouping) solution.  It uses nearest neighbour DNA binding thermodynamics to estimate unwanted pairings between PCR samples.

A tool to visualize the output from the database for annotation, visualization and integrated discovery DAVID in order to reveal overlapping biological connections for a list of relevant genes.

Norine has been and remains the unique resource dedicated to nonribosomal peptides (NRPs). It contains a database complemented with analysis tools (structure comparison, inference of monomer structure from chemical structure, mass spectrum analysis, NRP annotation for submission to the database). NRPs are secondary metabolites produced by bacteria and fungi and display a diverse spectrum of biological activity.