ANISEED is the main model organism database for the worldwide community of scientists working on a class of marine invertebrates, the tunicates (sister-group of vertebrates). It integrates for each species: a main knowledge base with extended information on gene function, gene expression, phylogeny and embryonic anatomy at single cell resolution; a genomic browser and a Genomicus gene synteny browser.

Annotation Retrieval of Gene Ontology Terms using semantic similarity in Gene Ontology.

ArrayExpress is a MIAME-standard compliant resource that stores functional genomics experiments performed using RNA-Seq/ChIP-Seq and array-based technologies.

arrayMap is a reference database and bioinformatics resource targeting copy number profiling data in human cancer. The database provides an entry point for meta-analysis and data integration of high-resolution oncogenomic CNA data. 

Alternative splicing database of human genes and functional annotation of their isoforms using the ASPic algorithm.

Database to retrieve and compare gene expression patterns between animal species. 

BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. 

ClustVis is a web tool for visualizing clustering of multivariate data. This web tool allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps.

Supports Finnish national data custodians (biobanks) in building a data resource for Sequence Initiative Suomi and affiliated projects.

Web based portal of organism-specific cross-platform expression compendia of bacterial organisms and grapevine

Aligns contigs from a draft genome to a closely related genome, and resolves their relative orientation based on this alignment.

A data resource for Quercus suber.

CRISPRCas++ is a new website holding a program called CRISPRCasFinder to detect CRISPR arrays and cas genes in the genome of prokaryotes. CRISPRCasMeta is adapted to the analysis of large metagenomic data. The programs are available online or can be downloaded for local usage. A database called CRISPRCasdb, the successor of CRISPRdb, is accessible on the CRISPRCas++ website. It can be browsed and queried in search for repeat and spacer sequences. 

Web interface for assignment and analysis of DNA conformers.

Database Of Local Biomolecumal COnfromers.

Produces and maintains automatic and manually curated annotation on eukaryotic genomes. It is integrated with important molecular resources, for example UniProt, and can be accessed programmatically or through a web browser.

Provides annotated genomes of farmed and domesticated animals in an easily viewable format via the Ensembl system.

Provides access to genome-scale data from bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces based on the Ensembl software platform.

An annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Pointers to positions in nucleotide sequence entries provide access to promoter sequences. 

European Variation Archive

The Expression Atlas allows users to search for gene expression changes measured in various cell types, organism parts, and disease states. It represents a curated subset of the ArrayExpress and GEO Archive experiments.

These include the Human Developmental Studies Network (HuDSeN), emouseatlas.org, echickatlas.org, and macrophages.com, a gene expression atlas of the domestic pig.

FAIDARE is a portal developed by ELIXIR-FR as an asset of the ELIXIR Plant Science community. FAIDARE enables data discovery through federations of distant Plant informations systems that have set up a standardized Restful API, the BrAPI. FAIDARE currently allows to do detailed searches of accessions and phenotyping data.

An optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data.

The Gene Ontology (GO) project addresses the need for consistent descriptions of gene products across databases. It has developed three structured, controlled vocabularies (ontologies) that describe gene products.

The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).

Genomicus is a database and a web server that integrates comparative genome data and ancestral genome reconstruction in a fast and intuitive way. It enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. A user-friendly graphical interface allows syntenic comparisons and gene order alignments between pairs of genomes or multiple genomes at different scales: local gene order, karyotypes, matrix plots, etc.  Different phylums such as Vertebrates, Plants, Fungi, Metazoa (as per Ensembl Genomes) are represented and regularly updated, as well as specific versions on Tunicates, Fish and Amphioxus.  

GnpIS is an interoperable Information System for plant and pest genomics. It is a powerful multispecies centralized information system with seven linked relational databases. 

The UniProt  GO annotation program (GOA) aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB).

Performs haplotype assembly from long gapless reads.