Services

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. 

MicroMiner searches mutations in protein structure databases like the PDB. Retrieved mutant structures can be easily analysed and compared. 

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.

A web application for validation of annotation of ligands and
residues.

The mOTUs tool uses phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) to profile microorganisms at species-level resolution when using metagenomic data as input. Since the MGs represent housekeeping genes, mOTUs can also be used to profile transcriptionally active community members when using metatranscriptomic data as input. Furthermore, MG-based SNV profiling provides an efficient alternative to using whole genome sequences to compare microbial strain populations.

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.

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 life science researchers to correct multiple hypothesis testing

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 platform linking gene expression changes and mutational status in solid tumours  

Nucleic acid search engine to reliably identify a wide range of modified RNA sequences.

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.

Enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.

Textmining tools

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.

The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping raw sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive world maps and ecological plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.

OMPdb is a database of beta-barrel outer membrane proteins from Gram-negative bacteria.