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欧洲生物信息学研究所(EMBL-EBI)的生物信息学网络及编程工具框架。

The EMBL-EBI bioinformatics web and programmatic tools framework.

作者信息

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

机构信息

European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK.

European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK

出版信息

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

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.

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7005/4489272/37d45683375b/gkv279fig1.jpg

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