All services

1000 Genomes

A deep catalog of shared human genetic variation in population groups worldwide.

ArrayExpress Archive of Functional Genomics Data

A database of functional genomics experiments including microarray and RNAseq expression data typically related to publications.

BioJS

A library of JavaScript components to represent biological data

BioModels database

A repository of peer-reviewed, published, computational models.

ChEMBL: Bioactive data for drug discovery

An open data resource of binding, functional and ADMET bioactivity data.

Chemical Entities of Biological Interest

Reference chemical structures, nomenclature and ontological classification.

Clustal Omega

Multiple sequence alignment of DNA or protein sequences. Clustal Omega replaces the older ClustalW alignment tools.

Clustal Phylogeny

Commonly used phylogenetic tree generation methods provided by the ClustalW2 program.

Complex Portal

The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms.

Database of Genomic Variants archive

A repository that provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species.

dbfetch

Programmatic-style retrieval of entries from EMBL-EBI databases

EBI BioSamples Database

A database describing biological samples and providing links to associated experimental data

EBI Metagenomics

Our Metagenomics service is a free-to-use, large-scale platform for analysis and archiving of metagenomic and metatranscriptome data. It provides a standardised analysis workflow, capable of producing rich taxonomic diversity and functional annotations, allowing analysis results to be compared both within and across projects at a broad level, and across different data types (for example, metagenomic and metatranscriptomic).

EBI Search

The EBI Search presents search results that are up-to-date with the data resources and provides an easy inter-domain navigation via a network of cross-references.

EMBOSS Tools

Selected EMBOSS tools for sequence analysis, providing: pairwise sequence alignment, sequence format conversion, sequence translation and back-translation, and sequence statistics.

ENA Sequence Search

ENA/SVA - Sequence Version Archive

Historical repository of EMBL-Bank entries

Ensembl

Ensembl enables and advances genome science by providing high-quality, integrated annotation on vertebrate genomes within a consistent and accessible infrastructure.

Ensembl Genomes

An integrating portal for genome-scale data from non-veterbrate species.

Enzyme Portal: Integrated enzyme data from EMBL-EBI resources

Integrated functional, sequence, nomenclature, substrate, product and cofactor data for enzymes.

Europe PubMed Central

Europe's life sciences literature database

European Genome-phenome Archive

A service for permanent archiving and sharing of all types of potentially identifiable genetic, molecular and phenotypic data resulting from biomedical research projects.

European Mouse Mutation Archive

A repository for the collection, archiving and distribution of relevant mouse mutant strains essential for basic biomedical research.

European Nucleotide Archive

An open, supported platform for the management, sharing, integration, archiving and dissemination of public-domain sequence data.

European Variation Archive

The European Variation Archive is an open-access database of all types of genetic variation data, from all species. The EVA provides access to highly detailed, granular, raw variant data from human, with other species to follow. All users can download data from any study, or submit their own data to the archive. You can also query all variants in the EVA by study, gene, chromosomal location or dbSNP identifier using our VCF Browser.

Experimental Factor Ontology

Data-driven application ontology for annotation and data visualisation

Expression Atlas

An added-value database that shows which genes/proteins are expressed under which conditions, and how expression differs between conditions.

FASTA [nucleotide]

Similarity search tool for nucleotide sequence databases.

FASTA [protein]

Similarity search tool for protein sequence databases.

FASTM [nucleotide]

Nucleotide fragment similarity search tool

FASTM [protein]

Peptide fragment similarity search tool

Gene Ontology

The Gene Ontology project aims to produce an unambiguous, universal language to describe biological phenomena across all species.

GeneWise

Compare a protein sequence to a genomic DNA sequence.

GGSEARCH [nucleotide]

Optimal global similarity search tool to search nucleotide databases for sequences homologous to your query.

GGSEARCH [protein]

Optimal global similarity search tool to search protein databases for sequences homologous to your query.

GLSEARCH [nucleotide]

Optimal global-query, local-database, similarity search tool to search nucleotide databases for sequences homologous to your query.

GLSEARCH [protein]

Optimal global-query, local-database, similarity search tool to search protein databases for sequences homologous to your query.

HMMER - protein homology search

Fast sensitive protein homology searches using profile hidden Markov models (HMMs). Variety of different search methods for querying against both sequence and HMM target databases.

HUGO Gene Nomenclature Committee

A database of approved gene symbols, names and associated data for human genes and their vertebrate orthologs.

Identifiers.org

Identifiers.org provides two connected services:

The Registry is a manually maintained registry of biomolecular data collections, for example UniProt. For each collection, it provides a list of its (possible more than one) location URLs, as well as regular expressions for identifier validation.

The Resolver maps URIs like http://identifiers.org/uniprot/P12345 to one of the actual URLs providing access to this collection. 

Thus, identifiers.org provides a curated infrastructure for the stable referencing of biomolecular entities in large scale data collections, buffering against changes of web addresses (URLs) for entities in biomolecular data resources.

IMGT/HLA

The IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System.

Infrafrontier-I3

The comprehensive resource for a European research network that is characterising, archiving and distributing mouse models of human disease.

IntAct Molecular Interaction Database

A freely available, curated database of molecular interactions.

Integrated GPCR bioactivity, sequence and structure data

Integrated bioactivity, sequence, structure and binding site data for rhodopsin-like GPCRs

Integrated Kinase biactivity, sequence and structure data

Integrated bioactivity, sequence, structure and binding site data for protein kinases.

IntEnz: Integrated relational enzyme database

Reference enzyme nomenclature and function.

International Mouse Phenotyping Consortium Portal

A centralised data centre and portal for gene-phenotype associations generated in an international effort to characterize a knockout mouse strain for over 20,000 mouse genes.

InterPro

A database for the classification of proteins into families, domains and conserved sites.

InterProScan 5

InterProScan 5 searches sequences against InterPro's predictive protein signatures. Please note that InterProScan 4.8 has been retired.

Job Dispatcher

JDispatcher is an analysis tool framework for job submission/dispatching and result retrieval/presentation

Kalign

Very fast multiple sequence alignment tool, suitable for large alignments.

LALIGN [nucleotide]

LALIGN finds internal duplications by calculating non-intersecting local alignments of protein or nucleotide sequences.

LALIGN [protein]

LALIGN finds internal duplications by calculating non-intersecting local alignments of protein or nucleotide sequences.

MAFFT

Multiple sequence alignment tool that uses Fast Fourier Transforms, suitable for medium alignments.

MapMi

Automated mapping and analysis of miRNA sequences across genomes

MEROPS

A database of proteolytic enzymes, their substrates and inhibitors.

MetaboLights: Metabolomics archive and reference database

A cross-species, cross-application, open-access, open-submission archive and reference database for metabolomics.

MUSCLE

Accurate multiple sequence alignment tool, especially good with proteins. Suitable for medium alignments.

MView

Transform a sequence similarity search result into a multiple sequence alignment or reformat a multiple sequence alignment.

NCBI BLAST [nucleotide]

Fast local similarity search tool for nucleotide sequence databases.

NCBI BLAST [protein]

Fast local similarity search tool for protein sequence databases.

NHGRI-EBI GWAS Catalog

The NHGRI-EBI GWAS Catalog is a quality-controlled, manually curated, literature-derived collection of all published genome-wide association studies. Co-developed with the NHGRI, it provides a karyotype visualisation of GWAS Catalog data. The GWAS Catalog is integrated with Ensembl and Europe PubMedCentral.

Ontology Lookup Service

OLS provides a unified interface to multiple ontologies on OBO format.

Patent databases

Non-redundant patent sequence databases providing access to full-text patent documents.

PDBe EM Resources

PDBe Electron Microscopy resources

PDBe NMR Resources

PDBe NMR resources

PDBeChem

A dictionary of chemical components referred to in PDB entries and maintained by the wwPDB.

PDBeFold

Provides interactive service for matching protein structures in 3D and looking for structural homologues in PDB and SCOP databases

PDBeMotif

Protein small structure motif search and statistics wrapped into integrated protein sequence and protein structure search

PDBePISA

protein interactions, surfaces and assemblies

Pfam

A database of conserved protein families and domains.

Phobius

Tool to predict transmembrane topology and signal peptides from the amino acid sequence of a protein.

PhytoPath

A resource for plant pathogen genomes.

PICR: The Protein Identifier Cross-Reference Service

Provides web services for mapping between protein identifier namespaces.

PomBase

A model organism database for Schizosaccharomyces pombe.

Pratt - Pattern Matching

Discover patterns in unaligned protein sequences.

PRIDE: The Proteomics Identifications Database

An archive of protein expression data determined by mass spectrometry.

PromoterWise

PromoterWise compares two DNA sequences allowing for inversions and translocations, ideal for promoters.

Protein Data Bank in Europe

The European resource for the collection, organisation and dissemination of 3D structural data (from PDB and EMDB) on biological macromolecules and their complexes.

PSI-BLAST

Fast iterative motif-based similarity search tool for proteins

PSI-Search

Highly accurate iterative motif-based similarity search tool for proteins combining sensitive Smith-Waterman searching with PSI-BLAST style iterations.

QuickGO

A web interface for browsing GO terms and annotations.

RADAR

Rapid Automatic Detection and Alignment of Repeats in protein sequences

Reactome pathways database

A manually curated, peer-reviewed database of biomolecular pathways.

Rfam

A database of covariance models and alignments to describe non-coding RNA families.

Rhea: Enzyme-catalysed reactions

A curated database of enzyme-catalysed reactions.

RNAcentral

RNAcentral is a database of non-coding RNA sequences that provides a single entry point for accessing the data from an international consortium of RNA resources.

SAPS - Statistical Analysis of Protein Sequences

Evaluate a wide variety of protein sequence properties

Sequence Checksum Generator

Generation of checksums for protein and nucleotide sequences.

SSEARCH [nucleotide]

Smith-Waterman sequence similarity search against nucleotide databases.

SSEARCH [protein]

Smith-Waterman sequence similarity search against protein databases.

Systems Biology Ontologies

Controlled vocabularies and ontologies for problems in systems biology.

T-Coffee

Consistency-based multiple sequence alignment tool that attempts to mitigate the pitfalls of progressive alignment methods. Suitable for small alignments.

Taxonomy services

Integrated taxonomic data and connection point for biomolecular data resources.

TreeFam

A database of phylogenetic trees of animal species to provide orthologue/paralogue definitions.

UniChem: Chemical Structure Cross-referencing

Rapid lookup of chemical structure objects across EMBL-EBI resources.

UniProt: The Universal Protein Resource

A comprehensive resource for protein sequence and functional annotation.

UniSave

A historical repository of UniProt entry versions.

VectorBase

An NIH-NIAID Bioinformatics Resource Centerfor invertebrate vectors of human patohgens.

Web Services

Programmatic access to various data resources and analysis tools via Web Services technologies.

Whatizit

Whatizit is a text processing system that allows you to do textmining tasks on text

Wise2DBA - DNA Block Aligner

Aligns two sequences under the assumption that the sequences share a number of colinear blocks of conservation separated by potentially large and varied lengths of DNA in the two sequences.

WormBase

A nematode-centric model organism database.