The EMBL-EBI bioinformatics web and programmatic tools framework

Weizhong Li, Andrew Cowley, Mahmut Uludag, Tamer Gur, Hamish McWilliam, Silvano Squizzato, Young Mi Park, Nicola Buso, Rodrigo Lopez*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

675 Scopus citations

Abstract

Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi. ac.uk/Tools/sss/) such as BLAST, FASTA and PSISearch, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically throughWeb Services interfaces (https://www.ebi.ac. uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, Inter-ProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community.

Original languageEnglish (US)
Pages (from-to)W580-W584
JournalNucleic acids research
Volume43
Issue numberW1
DOIs
StatePublished - Jan 1 2015

ASJC Scopus subject areas

  • Genetics

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