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  • Oxford University Press  (3)
  • 1
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    The EMBL-EBI bioinformatics web and programmatic tools framework (2015)
    Oxford University Press
    Details
    Publikationsdatum: 2015-07-02
    Beschreibung: 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.
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
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    The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI (2015)
    Oxford University Press
    Details
    Publikationsdatum: 2015-07-02
    Beschreibung: The European Bioinformatics Institute (EMBL-EBI— https://www.ebi.ac.uk ) provides free and unrestricted access to data across all major areas of biology and biomedicine. Searching and extracting knowledge across these domains requires a fast and scalable solution that addresses the requirements of domain experts as well as casual users. We present the EBI Search engine, referred to here as ‘EBI Search’, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. API integration provides access to analytical tools, allowing users to further investigate the results of their search. The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types including sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, together with relevant life science literature.
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
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    Analysis Tool Web Services from the EMBL-EBI (2013)
    Oxford University Press
    Details
    Publikationsdatum: 2013-06-23
    Beschreibung: Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services ( http://www.ebi.ac.uk/Tools/webservices/ ) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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