Service list

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. 

SNPmasker is a program to mask all SNPs in given sequence using information of dbSNP. Additionally it is possible to mask all non-unique words using GenomeMasker module.

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

Structural and physico-chemical interpretation of QSAR models

A database of RNA-binding splicing regulatory proteins reporting functional domains, protein and chemical interactors and expression data.

SQANTI3 is the first module of the [Functional IsoTranscriptomics (FIT)](https://tappas.org/) framework, which also includes IsoAnnot and tappAS.

Nextflow pipeline for splicing quantitative trait loci (sQTL) mapping based on sQTLseekeR2, performing the following analysis steps:

1. Index the genotype file
2. Preprocess the transcript expression data
3. Test for association between splicing ratios (a multivariate phenotype) and genetic variants in cis (nominal pass)
4. Obtain an empirical P-value for each phenotype (permutation pass, optional)
5. Control for multiple testing.

Analysis workflow for plant sRNA sequencing data.

Software for Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation.

 SSAM-lite is a lightweight, browser-based implementation of the SSAM framework. It provides the functionality of SSAMs most popular and widely used features in a graphical user interface with a few functions added for convenience and ease of use. It can be run on a modest laptop.

A validated reference peptide database for targeted proteomics. (Formerly QSDB)

Either as a cooperation or consultancy service.

• Cineca
• INFN
• GARR

STRING is a database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. 

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

SugarBind covers knowledge of glycan binding of human pathogen lectins and adhesins. Information is collected by experts from articles published in peer-reviewed scientific journals.

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.