title: The EMBL-EBI bioinformatics web and programmatic tools framework.
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 PSI-Search, 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 through Web 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+, InterProScan 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.
authors.affiliation: European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK.
authors.forename: Weizhong
authors.initials: W
authors.lastname: Li
authors.affiliation: European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Cowley
authors.affiliation: European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK.
authors.forename: Mahmut
authors.initials: M
authors.lastname: Uludag
authors.affiliation: European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK.
authors.forename: Tamer
authors.initials: T
authors.lastname: Gur
authors.affiliation: European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK.
authors.forename: Hamish
authors.initials: H
authors.lastname: McWilliam
authors.affiliation: European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK.
authors.forename: Silvano
authors.initials: S
authors.lastname: Squizzato
authors.affiliation: European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK.
authors.forename: Young Mi
authors.initials: YM
authors.lastname: Park
authors.affiliation: European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK.
authors.forename: Nicola
authors.initials: N
authors.lastname: Buso
authors.affiliation: European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK rls@ebi.ac.uk.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Lopez
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D020407:Internet; D016415:Sequence Alignment; D017421:Sequence Analysis; D012984:Software
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