Service list

StructureProfiler is a tool to screen structures based on selection criteria typically used upon dataset assembly for structure-based design methods.

SulfAtlas is a knowledge-based database which (i) helps to better annotate sulfatases in (meta)genomic data and notably to improve the prediction of substrate specificities; (ii) guides the experimental biologists to select target sulfatases which remain to be characterized in term of function and structure. The data contained in SulfAtlas is curated by experts, based on our phylogeny-based classification system and on literature.

SweeD is a high-performance computing software that detects the site of the beneficial mutation, using the Site Frequency Spectrum. It can analyze whole genome data of thousands of individuals in a few hours.

Database of protein expression time series for specific experiments on streptomyces, caulobacter, neiseria.

SWISS-MODEL Repository is a continuously updated database of annotated protein structure homology models generated by the fully automated SWISS-MODEL modelling pipeline. 

SWISS-MODEL is a fully automated service for protein structure homology modelling. It provides a personal web based workspace for interactive modelling, storing project data and visualizing results online. 

SwissBioPics is a freely available library of interactive biological images for visualizing subcellular location data. It includes cell types from all kingdoms of life - from muscle, neuronal and epithelial cells of animals to rods, cocci, clubs, spirals, and other more exotic forms of bacteria and archaea.

SwissDrugDesign provides a collection of web-based tools covering all aspects of computer-aided drug design.

A knowledge resource for lipids and their biology.

A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. 

SymCurv is a computational ab initio method for nucleosome positioning prediction. It is based on the structural property of natural nucleosome forming sequences, to be symmetrically curved around a local minimum of curvature.

Database of protein association networks representing a broad scala of biological associations between pairs of proteins that go beyond  direct protein interactions

TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.

Web tool for the prediction of T-cell receptor epitope recognition.

A training materials portal that helps you to discover, package and disseminate training resources. It aggregates training information from the ELIXIR nodes, and also from third-party content providers.

Transcription factor - target gene interaction and binding site database for multiple species

Contains tools for the functional classification of PLP-dependent enzymes in predicted protein sequences.

The European Nucleotide Archive (ENA) contains all the nucleotide sequences in the public domain and consolidates data from EMBL-Bank, the European Trace Archive and the Sequence Read Archive.

A web-based system for finding and testing relations between high-throughput sequencing and/or other genomic datasets (tracks), making use of statistical hypothesis testing and other advanced methodology.

The Ontology Lookup Service (OLS) provides a web service interface to query multiple ontologies from a single location with a unified output format.

Database of membrane localization of transmembrane protein structures estimated by AlphaFold2

A method for estimating the crystallizability of transmembrane proteins

Detection of transmembrane regions using 3D protein structure

Differential gene expression analysis in tumour, normal and metastatic tissues

Based on ICGC PanCancer infrastructure for organising and processing NGS data using workflow plugins including:  

• Workflow Plug-Ins - provide pipelines for the most common NGS processing tasks, including alignment (WES, WGS, WGBS, RNA-seq), quality control and variant calling (SNV, indel, CNV, SV).
• Cloud/HPC - IT Infrastructure for de.NBI users based on ICGC and TCGA PanCancer technology
• OTP - "One Touch Pipeline" is a comprehensive framework for NGS project organization and processing.
• Roddy - a framework for large scale NGS processing pipelines on Petabyte scale for the management of workflows in the Pan-Cancer Analysis of Whole Genomes (PCAWG) project.

Diverse tools under development, in use in BYOD events to facilitate making data FAIR using linked data technology.

Database of experimentally determined topological data of transmembrane proteins

The OpenMS Proteomics Pipeline making a range of tools available, including MetaProSIP and TOPPview. 

Visualising own data through OpenMS tools, including spectra, chromatograms, 2D LC-MS data and annotations. 

Training events about tools developed in ELIXIR-EE (usually g:Profiler, MEM, ClustVis are taught).