Web Services at EMBL-EBI

EMBL-EBI to be HTTPS by default from 1st October

On the 1st October the majority of services hosted on will be served over HTTPS by default. Services that are becoming HTTPS by default will automatically redirect users accessing the site on insecure HTTP URLs to secure HTTPS URLs. Users of EMBL-EBI services may wish to update links, bookmarks or API clients to use the HTTPS URLs.


These Web Services pages are being retired imminently for maintenance reasons. Replacement pages will be available at our confluence site as soon as this happens.

The EMBL-EBI provides programmatic access to various data resources and analysis tools via. Web Services technologies 1) 2) 3).

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 all users of EMBL-EBI Web Services to submit tool jobs in batches of no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with EMBL-EBI's Terms of Use. Please contact us if you need further information.

Chinese / 中文

敬告所有 EMBL-EBI Web Services 网络服务用户,请在呈交工具工作时,每批工作 不要超过30项,并请您在该批数据的结果和处理程序完成之后再呈交下一批工作。并请您提供一个有效的电子邮件地址。超额使用某项资源将按照 EMBL-EBI使用条款处理。 如需进一步信息,请通过此链接 与我们联系。

Korean / 한글

EMBL-EBI 웹서비스는 다량의 데이터(배치 등) 호출시, 사용자당 실시간으로 최대 30건의 처리를 제한적으로 사용하실 것을 권고드리고 있습니다. 보내신 건이 완료되기 전에, 재차 더 많은 데이터가 전송되지 않도록 협조 부탁드립니다. 또한 유효한 메일주소를 사용해주시기 바랍니다. 다량의 데이터 사용에 관한, EMBL-EBI 이용 약관을 준수해 주시것을 부탁드리며, 관련해 도움이 필요하시면, 문의 주시기 바랍니다.

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.

Data Retrieval

Service Clients Description
Array Express 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
EBI Search (formerly EB-eye) EBI Search (formerly EB-eye) 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
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.
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.
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
Simple Phylogeny (REST) Simple Phylogeny (SOAP) Neighbor-joining or UPGMA phylogenetic trees from an alignment using ClustalW2.

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 Analysis

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.

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.

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)
Ontology Lookup Service API 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


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Programmatic access to bioinformatics tools from EMBL-EBI update: 2017.
Nucleic Acids Res.
PubMed: 28431173
DOI: 10.1093/nar/gkx273
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The EMBL-EBI bioinformatics web and programmatic tools framework.
Nucleic Acids Res.
PubMed: 25845596
DOI: 10.1093/nar/gkv279
3) 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: 2017/09/15 14:23 by duggan