Services: Molecular And Cellular Structures

Regulatory Sequence Analysis Tools (RSAT) is a software suite combining specialised tools for the detection of regulatory signals in non-coding sequences. It includes tools for sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. The tools can be accessed via a Web site (http:rsat.eu/), as Web services, or installed locally on Linux / Mac OS X systems.

SIAMCAT is a modular framework for the statistical inference of associations between microbial communities and host phenotypes, such as disease states in clinical case-control studies. SIAMCAT is based on LASSO models, which offer distinctive advantages for model interpretation and microbial biomarker selection and avoid overfitting issues that can arise in naive combinations of feature selection and cross-validation. Part of the Microbiome Analysis Toolbox. 

SIDER is a web-based resource that contains information on marketed medicines and their recorded adverse drug reactions. This information is extracted from public documents and package inserts. SIDER makes available side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations. It currently covers associations between 5,868 side effects and 1,430 drugs. Part of the Human Omics Analysis Toolbox. 

The SIGnaling Network Open Resource annotates signaling information from the literature as binary causative relationships.

Web application to compare multiple protein structural motifs.

SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains via sequence homology searches. It contains manually curated models for more than 1,200 protein domains. In its ‘Genomic’ mode, it annotates proteins from completely sequenced genomes of 2,031 species as a basis for their functional annotation. It provides flexible tools to visually explore protein domain architectures across sequences and organisms. Part of the Human Omics Analysis Toolbox. 

Prediction of single point protein mutations likely to be involved in disease.

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. 

Detection of transmembrane regions using 3D protein structure

Differential gene expression analysis in tumour, normal and metastatic tissues

The glycomic MS database and repository.

Collection of validation results for the entire Protein Data Bank.

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.

Atlas of Protein Hydration

Workflow4Metabolomics resource is based on the Galaxy environment that provides user-friendly interfaces to build, run, and share comprehensive data analysis workflows and gives access to a High Performance Computing environment the ELIXIR-FR/IFB infrastructure. Thus, W4M offers more than 40 tools to process data from all three main technologies (NMR, GCMS, LCMS), including unique algorithms developed by the W4M developers themselves. Data and workflows can be re-used and publicly shared, thus becoming useful references for the community. Finally, the platform provides many tutorials and a help desk.