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Nucleic Acids Res. 2015 Jul 1;43(W1):W580-4. doi: 10.1093/nar/gkv279. Epub 2015 Apr 6.

The EMBL-EBI bioinformatics web and programmatic tools framework.

Author information

1
European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK.
2
European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK rls@ebi.ac.uk.

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.

PMID:
25845596
PMCID:
PMC4489272
DOI:
10.1093/nar/gkv279
[Indexed for MEDLINE]
Free PMC Article

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