Popular services

IntAct Molecular Interaction Database

A curated database of molecular interactions.

UniProt: The Universal Protein Resource

A comprehensive resource for protein sequence and functional annotation.

Complex Portal

A manually curated, encyclopaedic resource of macromolecular complexes from model organisms.

PRIDE: The Proteomics Identifications Database

An archive of protein expression data determined by mass spectrometry.

InterPro

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

Pfam

A database of conserved protein families and domains.

Clustal Omega

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

HMMER - protein homology search

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

InterProScan

InterProScan searches sequences against InterPro's predictive protein signatures.

BLAST [protein]

Fast local similarity search tool for protein sequence databases.

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.

Clustal Phylogeny

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

All services

BioJS

The open-source JavaScript visualisation library for life-science data.

BLAST [protein]

Fast local similarity search tool for protein sequence databases.

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

A manually curated, encyclopaedic resource of macromolecular complexes from model organisms.

EMBOSS Tools

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

Enzyme Portal: Integrated enzyme data from EMBL-EBI resources

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

FASTA [protein]

Sequence search for protein sequences

FASTM [protein]

Peptide fragment similarity search tool

GeneWise

Compare a protein sequence to a genomic DNA sequence.

GGSEARCH [protein]

Optimal global similarity search tool to search protein 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) for querying against both sequence and HMM target databases.

IntAct Molecular Interaction Database

A curated database of molecular interactions.

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 searches sequences against InterPro's predictive protein signatures.

Kalign

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

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.

MView

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

Patent databases

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

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.

PICR: The Protein Identifier Cross-Reference Service

Provides web services for mapping between protein identifier namespaces.

Pratt - Pattern Matching

Discover patterns in unaligned protein sequences.

PRIDE: The Proteomics Identifications Database

An archive of protein expression data determined by mass spectrometry.

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

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

RADAR

Rapid Automatic Detection and Alignment of Repeats in protein sequences

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.

SSEARCH [protein]

Smith-Waterman sequence similarity search against protein databases.

T-Coffee

Consistency-based multiple sequence alignment tool.

TreeFam

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

UniProt: The Universal Protein Resource

A comprehensive resource for protein sequence and functional annotation.

UniSave

A historical repository of UniProt entry versions.

Project websites

IMPACT

The IMPACT Project (IMproving Protein Annotation through Coordination and Technology) was a 3 year, EU-funded project to continue to develop and enhance InterPro and its contributing databases (Gene3D, Pfam, PRINTS, ProDom, Prosite, SMART, SuperFamily).

Reference Proteomes