Web Services at EMBL-EBI


The EMBL-EBI provides programmatic access to various data resources and analysis tools via. Web Services technologies 1) 2).

Web Services is an integration and inter-operation technology. To ensure client and server software from various sources will work well together, the technology is built on open standards:

For the transport layer Web Services utilise common network protocols, typically the Hypertext Transfer Protocol (HTTP) used to provide access to web sites.

For an overview of Web Services technologies and short tutorials on using common programming languages and Web Services tool-kits see Introduction to Web Services.

Important Note

We kindly ask users to submit NO MORE THAN 30 JOBS AT THE TIME AND NOT TO SUBMIT MORE JOBS UNTIL YOU HAVE OBTAINED RESULTS FOR THE LAST 30. There are many people using these services and a fair share policy has been implemented that allows us to block users that submit jobs in a manner that prevents others from using the service. This block may affect access to the EMBL-EBI Web Services for an entire organisation or a class B or C subnet. Also make sure you USE A REAL EMAIL ADDRESS in your submissions. Using a fake email means we cannot contact you and will very likely result in your jobs being killed and your IP, Organisation or entire domain being black-listed. We do apologise for any inconvenience this may cause.

Web Services

A list of Web Services provided by EMBL-EBI follows. For services from other providers (e.g. DDBJ, KEGG, NCBI, etc.) see services registries such as BioCatalogue or seekda.

Data Retrieval

Service Clients Description
ArrayExpress Microarray data searching with ArrayExpress.
ChEBI Web Services ChEBI Web Services Entry retrieval from the ChEBI database.
ChEMBL Web Services ChEMBL Web Services Search data in, and retrieve data from the ChEMBL database
EB-eye (SOAP) EB-eye (SOAP) Database search using the EBI Search search engine (EB-eye).
EB-eye (REST) EB-eye (REST) Database search using the EBI Search search engine (EB-eye).
ENA Browser Retrieval of sequence and associated records from ENA
Gene Expression Atlas API Enriched database of summary statistics over a curated subset of ArrayExpress Archive
MartService Database search and data retrieval using BioMart.
PDBe (REST) PDBe’s REST API is a programmatic way to obtain information from the PDB and EMDB.
PSICQUIC Standardised access to molecular interaction databases, including ChEMBL, Reactome and IntAct.
Rhea Manually annotated database of chemical reactions The Universal Protein Resource (UniProt) a comprehensive resource for protein sequence and annotation data.
WSDbfetch (REST) WSDbfetch (REST) Identifier based entry retrieval for various up-to-date biological databases.
WSDbfetch (SOAP) WSDbfetch (SOAP) Identifier based entry retrieval for various up-to-date biological databases.

Protein Functional Analysis (PFA)

REST Service SOAP Service Description
FingerPRINTScan (REST) FingerPRINTScan(SOAP) Identifying the closest matching PRINTS sequence motif fingerprints in a protein sequence.
InterProScan 5 (REST) InterProScan 5 (SOAP) A tool that combines different protein signature recognition methods.
HMMER hmmscan (REST) HMMER hmmscan (SOAP) Search a database of Hidden Markov Models (HMMs) with a sequence to infer membership of a sequence family.
PfamScan (REST) Pfamscan (SOAP) PfamScan is used to search a FASTA sequence against a library of Pfam HMM.
Phobius (REST) Phobius (SOAP) Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein.
Pratt (REST) Pratt (SOAP) Search for patterns conserved in sets of unaligned protein sequences.
PROSITE Scan (REST) PROSITE Scan (SOAP) Comparing a protein sequence against the signatures in PROSITE (both patterns and profiles).
RADAR (REST) RADAR (SOAP) Detection and alignment of repeats in protein sequences.

Sequence Similarity Search (SSS)

Identify potentially homologous sequences based on sequence similarity.

REST Service SOAP Service Description
FASTA (REST) FASTA (SOAP) Fast protein or nucleotide comparison using the FASTA suite. Includes Smith and Waterman local-local (SSEARCH), global-local (GLSEARCH) and global-global (GGSEARCH) alignment searches.
FASTM (REST) FASTM (SOAP) Peptide fragment searches using the FASTF, FASTM or FASTS programs from the FASTA suite.
NCBI BLAST (REST) NCBI BLAST (SOAP) Compare a sequence with those contained in nucleotide and protein databases using NCBI BLAST.
PSI-BLAST (REST) PSI-BLAST (SOAP) Position Specific Iterative BLAST (PSI-BLAST), guided mode
PSI-Search (REST) PSI-Search (SOAP) Iterative Smith and Waterman using a PSI-BLAST strategy
HMMER (REST) Fast, sensitive search using HMMER suite. Includes phmmer, hmmscan, hmmsearch and jackhmmer

Multiple Sequence Alignment (MSA)

Alignment of a set of three or more, protein or nucleotide sequences.

REST Service SOAP Service Description
Clustal Omega (REST) Clustal Omega (SOAP) Protein, DNA and RNA multiple sequence alignment using Clustal Omega.
ClustalW2 (REST) ClustalW2 (SOAP) Global multiple sequence alignment of DNA and protein sequences using ClustalW 2.
DbClustal (REST) DbClustal (SOAP) Global multiple sequence alignment of DNA or protein sequences using anchor regions from BLAST results
Kalign (REST) Kalign (SOAP) Sequence alignment using the Kalign method. Fast and accurate algorithm, which handles large sequences.
MAFFT (REST) MAFFT (SOAP) Sequence alignment using the MAFFT method. Fast and capable of handling large sequences.
MUSCLE (REST) MUSCLE (SOAP) Sequence alignment using the Multiple Sequence Comparison by Log-Expectation (MUSCLE) method.
MView (REST) MView (SOAP) Reformat a multiple sequence alignment or create a multiple sequence alignment from a sequence similarity search result (e.g. BLAST or FASTA).
PRANK (REST) PRANK (SOAP) Sequence alignment using the PRANK method.
T-Coffee (REST) T-Coffee (SOAP) Sequence alignment using the T-Coffee method.


REST Service SOAP Service Description
ClustalW2 Phylogeny (REST) ClustalW2 Phylogeny (SOAP) Neighbor-joining or UPGMA phylogenetic trees from an alignment using ClustalW 2.

Pairwise Sequence Alignment (PSA)

Alignment of two sequences.

REST Service SOAP Service Description
EMBOSS matcher (REST) EMBOSS matcher (SOAP) Waterman-Eggert local alignment using EMBOSS matcher.
EMBOSS needle (REST) EMBOSS needle (SOAP) Needleman-Wunsch global alignment using EMBOSS needle.
EMBOSS stretcher (REST) EMBOSS stretcher (SOAP) Myers and Miller global alignment using EMBOSS stretcher.
EMBOSS water (REST) EMBOSS water (SOAP) Smith-Waterman local alignment using EMBOSS water.
GeneWise (REST) GeneWise (SOAP) Comparing a protein sequence to a genomic DNA sequence.
lalign (REST) lalign (SOAP) Huang and Miller sim local alignment using lalign.
PromoterWise (REST) PromoterWise (SOAP) Comparing two DNA sequences allowing for inversions and translocations, ideal for promoters.
Wise2DBA (REST) Wise2DBA (SOAP) The Wise2 DNA Block Aligner (DBA) aligns two DNA sequences.


RNA Anslysis

REST Service SOAP Service Description
Infernal cmscan (REST) Infernal cmscan(SOAP) Infernal cmscan is used to search the CM-format Rfam database.
MapMi (REST) MapMi (SOAP) Mapping and analysis of miRNA sequences.

Sequence Format Conversion

Convert between common sequence formats, or verify the formatting of a sequence.

REST Service SOAP Service Description
EMBOSS seqret (REST) EMBOSS seqret (SOAP) Manipulation of sequence entries, including conversion between sequence data formats.
MView (REST) MView (SOAP) Reformatting of multiple sequence alignment data.
Readseq (REST) Readseq (SOAP) Convert biosequences between a selection of common biological sequence formats.

Sequence Statistics

Analyse a sequence to determine its properties and use statistics to assign significance.

REST Service SOAP Service Description
EMBOSS cpgplot (REST) EMBOSS cpgplot (SOAP) EMBOSS cpgplot identifies and plots CpG islands in nucleotide sequence.
EMBOSS isochore (REST) EMBOSS isochore (SOAP) EMBOSS isochore plots isochores in DNA sequences.
EMBOSS pepinfo (REST) EMBOSS pepinfo (SOAP) EMBOSS pepinfo plots amino acid properties.
EMBOSS pepstats (REST) EMBOSS pepstats (SOAP) EMBOSS pepstats calculates protein properties such as molecular weight.
EMBOSS pepwindow (REST) EMBOSS pepwindow (SOAP) EMBOSS pepwindow generates a hydropathy plot for a protein.
SAPS (REST) SAPS (SOAP) Statistical Analysis of Protein Sequences (SAPS).

Sequence Translation

Translate a coding nucleotide sequence in to a protein sequence, or back-translate from a protein sequence to a possible coding nucleotide sequence.

REST Service SOAP Service Description
EMBOSS transeq (REST) EMBOSS transeq (SOAP) EMBOSS transeq translates nucleic acid sequences to the corresponding peptide sequences.
EMBOSS sixpack (REST) EMBOSS sixpack (SOAP) EMBOSS sixpack displays DNA sequences with 6-frame translation and ORFs.
EMBOSS backtranseq (REST) EMBOSS backtranseq (SOAP) EMBOSS backtranseq back-translates protein sequences to nucleotide sequences.
EMBOSS backtranambig (REST) EMBOSS backtranambig (SOAP) EMBOSS backtranambig back-translates protein sequences to ambiguous nucleotide sequences.

Structural Analysis

Analysis of macromolecular structures.

REST Service SOAP Service Description
DaliLite (REST) DaliLite (SOAP) Pairwise structure comparison.
MaxSprout (REST) MaxSprout (SOAP) Fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace.

Literature and Ontologies

Look-up ontology terms and navigate ontology relationships or access and analyse the literature.

Service Clients Description
BioModels BioModels Storing, searching and retrieving published mathematical models of biological interest
PICR Protein Identifier Cross-Reference Service
QuickGO QuickGO Gene Ontology (GO) and Gene Ontology Annotation (GOA) databases
Europe PMC Web Service Search Europe PubMed Central
WSMIRIAM Web Services for the Minimal Information Requested In the Annotation of biochemical Models (MIRIAM)
WSOntology Lookup Search multiple ontologies from a single location with a unified output format
WSSBO WSSBO Web Services for the Systems Biology Ontology (SBO)
WSWhatizit WSWhatizit A text processing system that allows you to do text mining tasks on text


1) Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R. (2015)
The EMBL-EBI bioinformatics web and programmatic tools framework.
Nucleic Acids Res.
PubMed: 25845596
DOI: 10.1093/nar/gkv279
2) Lopez R, Cowley A, Li W, McWilliam H. (2014)
Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.
Curr Protoc Bioinformatics. 2014;48 3.12.1-3.12.50.
PubMed: 25501941
DOI: 10.1002/0471250953.bi0312s485
about/webservices.txt · Last modified: 2015/10/30 11:31 by apc