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. 

Automated high-throughput assembly, annotation and feature analysis of microbial genome cohorts

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

BacDive represents a collection of organism-linked information covering the multifarious aspects of bacterial and archaeal biodiversity. The content encloses information on taxonomy, morphology, physiology, sampling and environmental conditions as well as molecular biology.

Online access to tools and databases related to miRNAs binding site predictions, RNA Binding protein binding sites, circular RNAs, CLIP data analysis and transcriptome analysis

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. 

Chipster is a user-friendly analysis software for high-throughput data. It contains hundreds of analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. 

DELLY discovers germline and somatic structural variants in short-read massively parallel sequencing data

DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution. Part of the Human Omics Analysis Toolbox

DEXSeq is an extension of DESeq for the analysis of alternative exon usage. DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution. Part of the Human Omics Analysis Toolbox

Web interface for assignment and analysis of DNA conformers.

Database Of Local Biomolecumal COnfromers. (Formerly known as DOLCE)

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.

Enterotypes are densely populated regions in a high-dimensional space of microbiome community composition, by which human individuals can be stratified. Computational methods to detect and characterise enterotypes in any dataset, either to reproduce previous reports or determine enterotypes in new studies, are provided and explained. Part of the Microbiome Analysis Toolbox. 

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.