Other software

Popular services

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.

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.

InterProScan 5

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

NCBI BLAST [protein]

Fast local similarity search tool for protein sequence databases.

PDBeFold

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

PDBePISA

protein interactions, surfaces and assemblies

Ontology Lookup Service

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

All services

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.

ClustalW2

Multiple sequence alignment of DNA or protein sequences. Clustal Omega often produces better results than ClustalW2.

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 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.

Enzyme Portal: Integrated enzyme data from EMBL-EBI resources

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

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.

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.

InterProScan 5

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

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.

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.

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

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.

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.

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.

RADAR

Rapid Automatic Detection and Alignment of Repeats in protein sequences

Readseq

Conversion between common biological sequence formats.

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.

T-Coffee

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

Web Services

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

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.

WU-BLAST [nucleotide]

Sequence similarity search of nucleotide databases using WU-BLAST.

WU-BLAST [protein]

Sequence similarity search of protein databases with WU-BLAST.