European Bioinformatics Institute (EMBL-EBI)

Proteins API REST
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The Proteins REST API provides access to key biological data from UniProt and data from Large Scale Studies data mapped to UniProt. The services provide sequence feature annotations from UniProtKB, variation data from UniProtKB and mapped from Large Scale data sources (1000 Genomes, ExAC and COSMIC), proteomics data mapped from Large Scale sources (PeptideAtlas, MaxQB and EPD) and genome coordinate mappings.The interactive documentation provides dynamically generated source code for Java, P...

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/proteins/api

CRAM reference registry: sequence retrieval by MD5 and SHA1 REST Gb
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The CRAM reference registry provides access to reference sequences used in CRAM files. Retrieval of reference sequences from the CRAM reference registry is provided by MD5 or SHA1 checksum and through no other means. Please note that all sequences in the registry are fully public but are not retrievable without knowing the MD5 or SHA1 checksums.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/ena/cram

Europe PMC RESTful Web Service for Articles REST Gb
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The Europe PMC RESTful Web Service gives you access to all of the publications and related information held in the Europe PMC database, which includes the following: 1. Over 30 million publications from various sources, including PubMed, AGRICOLA, and the European Patent Office. 2. Provision of the full text article free for more than 3 million of these publications, of which more than 900,000 are open access. 3. Database cross-references to a number of databases, including UniProt, the ...

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/europepmc/webservices/rest

Europe PMC SOAP Web Service SOAP Gb
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This web service gives programmatic access to all of the publications and related information in Europe PubMed Central (Europe PMC). The following is included: 1. Over 30 million abstracts from CiteXplore, including PubMed, Agricola, and international Patents from the European Patent Office. Section 3 provides background information about the data sources. 2. Over 3 million full text articles from PubMed Central, of which 900 thousand are open access. 3. Database crosslinks to a numbe...

Provider: European Bioinformatics Institute (EMBL-EBI) | WSDL Location: http://www.ebi.ac.uk/europepmc/webservices/soap?wsdl

EMBOSS Backtranambig REST Gb
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EMBOSS backtranambig reads a protein sequence and writes the nucleic acid sequence it could have come from. It does this by using nucleotide ambiguity codes that represent all possible codons for each amino acid.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/emboss_backtranambig

EMBOSS Backtranseq REST Gb
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EMBOSS backtranseq reads a protein sequence and writes the nucleic acid sequence it is most likely to have come from.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/emboss_backtranseq

EMBOSS Sixpack REST Gb
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EMBOSS sixpack reads a DNA sequence and outputs the three forward and (optionally) three reverse translations in a visual manner.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/emboss_sixpack

EMBOSS Transeq REST Gb
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EMBOSS transeq translates nucleic acid sequences to their corresponding peptide sequences. It can translate to the three forward and three reverse frames, and output multiple frame translations at once.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/emboss_transeq

SAPS REST Gb
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SAPS (Statistical Analysis of Protein Sequences) evaluates a wide variety of protein sequence properties using statistics.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/saps

EMBOSS pepstats REST Gb
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EMBOSS pepstats calculates statistics for a protein such as molecular weight and isoelectric point.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/emboss_pepstats

Readseq REST Gb
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Readseq reads and converts biosequences between a selection of common biological sequence formats, including EMBL, GenBank and fasta sequence formats.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/readseq

EMBOSS seqret REST Gb
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EMBOSS seqret reads and writes (returns) sequences. It is useful for a variety of tasks, including extracting sequences from databases, displaying sequences, reformatting sequences, producing the reverse complement of a sequence, extracting fragments of a sequence, sequence case conversion or any combination of the above functions.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/emboss_seqret

MapMi REST Gb
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MapMi is a tool for mapping and analysis of miRNA sequences. It is designed to locate miRNA precursor sequences in existing genomic sequences (e.g Ensembl and Ensembl Metazoa), using potential mature miRNA sequences as input. After searching the genome for the provided mature sequences, these hits are extended and classified taking into account major structural properties of known miRNA precursors.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/mapmi

Infernal cmscan REST Gb
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Infernal cmscan is used to search the CM-format Rfam database.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/infernal_cmscan

Wise2DBA REST Gb
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The Wise2 DNA Block Aligner (DBA) aligns two DNA sequences using 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.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/wise2dba

PromoterWise REST Gb
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PromoterWise compares two DNA sequences allowing for inversions and translocations, ideal for promoters.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/promoterwise

GeneWise REST Gb
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GeneWise compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/genewise

Clustal Omega REST Gb
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Clustal Omega is a multiple sequence alignment program for protein sequences.

Provider: European Bioinformatics Institute (EMBL-EBI) | Base URL: http://www.ebi.ac.uk/Tools/services/rest/clustalo