The EMBL-EBI bioinformatics web and programmatic tools framework

By Weizhong Li, Andrew Peter Cowley, Mahmut Uludag, Tamer Gur, Hamish McWilliam, Silvano Squizzato, Young M. Park, Nicola Buso, Rodrigo Lopez. Nucleic Acids Res., 2015

1,016 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/32dc2a2ea7d1735b3c0cf5f782200453215fe6cd

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In Molecular Biology

Citations in the corpus

Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services (2014, methodology): “Since 1995, the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools using web services technologies (Chojnacki, Cowley, Lee, Foix, & Lopez, 2017; Li et al., 2015; Madeira et al., 2019; McWilliam et al., 2013).”
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis (2016, background): “org), the EMBL-EBI Bioinformatics Web Services [(1); http://www.”
LINE-1 derepression in senescent cells triggers interferon and inflammaging (2019, neutral): “Second, a consensus sequence of these 6 sequences was generated with the Clustal Omega multiple sequence alignment tool (http://www.ebi.ac.uk/Tools/msa/clustalo/) 39 .”
The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes (2016, background): “…Institute of the 74 European Molecular Biology Laboratory (EMBL-EBI), the U.S. National Center for Biotechnology 75 Information (NCBI) E-Utilities, the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the M5nr 76 (Kanehisa & Goto, 2000; Sayers et al., 2009; Wilke et al., 2012; Li et al., 2015).”