Services

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. 

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

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.

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

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.

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.

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. 

Template-based RNA secondary structure visualization.

A multiple sequence alignment package that can be used for DNA, RNA and protein sequences. It can be used to align sequences or to combine the output of other alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment.

Trimmomatic is a flexible read trimming tool for NGS data.

Platform for metaproteomics data analysis with a focus on interactive data visualizations

UniProt Related Documents (UniReD): assisting wet lab biologists
in their quest on finding novel counterparts in a protein network

Tools for processing the topology and structure of transmembrane proteins

• A. Constrained Consensus TOPology prediction server (CCTOP) 
• B. Transmembrane helices and protein topology prediction (HMMTOP),
• C. Detection of transmembrane regions (TMDET)
• D. Transmembrane proteins’ membrane segments folding recognizing (TmFoldWeb)

Public Galaxy instance enabling reproducible data analysis through workflows

V-pipe is the bioinformatics pipeline that integrates various open-source software packages for assessing viral genetic diversity from next-generation sequencing (NGS) data derived from intra-host virus populations. V-pipe enables reliable and comparable viral pathogen genomics and epidemiological studies and facilitates clinical diagnostics of viruses.

VarAFT is a software designed to annotate and filter Human NGS data. This system was developed within the RD-Connect project and was instrumental for the creation of the RD-Connect Genome-Phenome platform. As a stand-alone java system, it ensures full data protection, critical for clinical use. VarAFT provides experiments’ quality, annotates, and allows the filtration of VCF files. Data from multiple samples can be combined to address different Mendelian Inherited Disorders, Population Genetics or Cancers. It contains unique variant priorization features including OMIM, HPO, Gene Ontology, pathways and predictions from UMD-Predictor and Human Splicing Finder in addition to classical annotations from dbNSFP . It is used by many research and clinical laboratories worldwide.

Performs ranking of variants in genomic datasets, integrating information from multiple sources to prioritize each variant by its deleteriousness, novelty and existing information.

Accurate validation, mapping and formatting of sequence variant descriptions

A high recall search engine to support the curation of genomic variants.

https://academic.oup.com/bioinformatics/article/38/9/2595/6547047

Galaxy server for the functional annotation and prioritization of genetic variants.

WarPP is a fully automated procedure to place water molecules in the active site of a protein structure. 

A web-accessible, single cell RNA-Seq processing platform designed for the management, analysis and interpretation of scRNA-seq high-throughput data.

A software package for the automatic discovery of enriched motifs in a set of related DNA sequences, including ChIP-Seq peaks.