Service teams

1000 Genomes A deep catalog of shared human genetic variation in population groups worldwide.

ArchSchema Interactive graphs of Pfam domain architecture networks

ArrayExpress Archive of Functional Genomics Data A database of functional genomics experiments including microarray or 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.

CENSOR A tool that screens query sequences against a reference collection of repeats.

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 A new multiple sequence alignment tool using HMM-HMM profiles, suitable for medium-large alignments.

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

ClustalW2 Multiple sequence alignment with ClustalW2.

DaliLite DaliLite computes optimal and suboptimal structural alignments between two protein structures.

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

DbClustal Create a multiple sequence alignment from a protein BLAST result.

dbfetch Programmatic-style retrieval of entries from EMBL-EBI databases

Distributed Annotation System (sensu protein sequences) DAS provides client-side integration of protein sequence annotation.

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

EBI Metagenomics A resource for the analysis and archiving of metagenomic data.

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/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 A comprehensive archive of submitted nucleotide sequence read, assembly and functional annotation data

Experimental Factor Ontology Data-driven application ontology for annotation and data visualisation

Expression Atlas An added-value database that shows which genes 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

FingerPRINTScan Search PRINTS with a protein query sequence.

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.

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

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.

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

InterProScan InterProScan is a software package that allows users to search their sequences against the InterPro database's predictive protein signatures.

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.

MaxSprout MaxSprout generates protein backbone and side chain co-ordinates from a C(alpha) trace.

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.

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

Pfam A database of hidden Markov models and alignments to describe conserved protein families and domains.

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

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.

PROSITE Scan Search a protein query sequence for protein motifs using the patterns and profiles in PROSITE.

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.

RADAR Rapid Automatic Detection and Alignment of Repeats in protein sequences

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

Readseq Conversion between common biological sequence formats.

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.

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.

SRS - Sequence Retrieval System Advanced querying of EMBL-EBI databases.

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.

The International Mouse Phenotyping Consortium 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.

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

UniChem: Chemical Structure Cross-referencing Rapid lookup of EBI chemical structure objects across resources

UniProt: The Universal Protein Resource The gold-standard, comprehensive resource for protein sequence and functional annotation data.

UniSave A historical repository of UniProtKB 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.

WormBase A nemoatode-centric model organism database.

WU-BLAST [nucleotide] Sequence similarity search of nucleotide databases using WU-BLAST.

WU-BLAST [protein] Sequence similarity search of protein databases with WU-BLAST.