Services: Genes And Genomes

Analysis workflow for plant sRNA sequencing data.

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

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.

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.

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.

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.

Differential gene expression analysis in tumour, normal and metastatic tissues

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.

Type (Strain) Genome Server allows you to identify or classify prokaryotic strains and provides genome-based phylogenies with branch support, (sub-)species delineation via digital DDH, differences in genomic G+C content and much more.

Curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, with experimentally validated functional motifs and cross-links to interacting regulatory proteins.

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 resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries. 

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.

WheatIS is a portal that enables data discovery through an international federation of distant informations systems about wheat genetics and genomics in the frame of the Wheat Initiative (www.wheatinitiative.org). The WheatIS portal allows a keyword-based discovery of any type of data. It currently gives a single entry point to data provided by twelve different worldwide institutes.

An open, collaborative platform dedicated to the curation of biological pathways

Federated genomics data sharing platform allowing users to query genomic and phenotypic information.

Workflow Execution Service automating a number of steps, including: 

1. Fetch and cache a workflow a number of sources
2. Identify the kind of workflow.
3. Fetch and set up workflow execution engine
4. Identify the needed containers by the workflow
5. Execute the workflow in a secure way

Repository of regulatory associations between transcription factors and target genes in Saccharomyces cerevisiae.