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. 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

Weizhong Li  1 , Andrew Cowley  1 , Mahmut Uludag  1 , Tamer Gur  1 , Hamish McWilliam  1 , Silvano Squizzato  1 , Young Mi Park  1 , Nicola Buso  1 , Rodrigo Lopez  2
Affiliations

The EMBL-EBI bioinformatics web and programmatic tools framework

Weizhong Li et al. Nucleic Acids Res. .

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.

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Figures

Figure 1.
Figure 1.
An example workflow from NCBI BLAST+ to Clustal Omega and construction of a phylogenetic tree. (a) Perform a NCBI BLAST+ similarity search and select sequence hits from the summary table to align with Clustal Omega; (b) Perform a simple phylogenetic analysis on the Clustal Omega alignment; (c) Visualise the phylogenetic tree.
Figure 2.
Figure 2.
An example domain display from PSI-Search output, showing UniProt sequence features that are present in significantly aligned regions.
See this image and copyright information in PMC

References

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