SLiMSearch 2.0 : biological context for short linear motifs in proteins

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dc.contributor.author Davey, Norman E.
dc.contributor.author Haslam, Niall J.
dc.contributor.author Shields, Denis C.
dc.contributor.author Edwards, Richard J.
dc.date.accessioned 2011-09-27T13:22:59Z
dc.date.available 2011-09-27T13:22:59Z
dc.date.copyright The Author(s) 2011 en
dc.date.issued 2011-05-26
dc.identifier.citation Nucleic Acids Research en
dc.identifier.uri http://hdl.handle.net/10197/3180
dc.description.abstract Short, linear motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch 2.0 (Short, Linear Motif Search) web server allows researchers to identify occurrences of a user-defined SLiM in a proteome, using conservation and protein disorder context statistics to rank occurrences. User-friendly output and visualizations of motif context allow the user to quickly gain insight into the validity of a putatively functional motif occurrence. For each motif occurrence, overlapping UniProt features and annotated SLiMs are displayed. Visualization also includes annotated multiple sequence alignments surrounding each occurrence, showing conservation and protein disorder statistics in addition to known and predicted SLiMs, protein domains and known post-translational modifications. In addition, enrichment of Gene Ontology terms and protein interaction partners are provided as indicators of possible motif function. All web server results are available for download. Users can search motifs against the human proteome or a subset thereof defined by Uniprot accession numbers or GO term. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch2.html. en
dc.description.sponsorship Science Foundation Ireland en
dc.description.sponsorship European Research Council en
dc.description.sponsorship Other funder en
dc.format.extent 874228 bytes
dc.format.mimetype application/pdf
dc.language.iso en en
dc.publisher Oxford University Press en
dc.relation.requires CASL Research Collection en
dc.relation.requires Conway Institute Research Collection en
dc.relation.requires School of Medicine & Medical Science Research Collection en
dc.subject Linear motif en
dc.subject Protein protein interactions en
dc.subject Minimotifs en
dc.subject.lcsh Protein-protein interactions en
dc.subject.lcsh Proteins--Research--Data processing en
dc.subject.lcsh Proteins--Research--Technological innovations en
dc.subject.mesh Protein Interaction Domains and Motifs en
dc.subject.mesh Computing Methodologies en
dc.title SLiMSearch 2.0 : biological context for short linear motifs in proteins en
dc.type Journal Article en
dc.internal.availability Full text available en
dc.internal.webversions Publisher's version
dc.internal.webversions http://dx.doi.org/10.1093/nar/gkr402
dc.status Peer reviewed en
dc.identifier.volume 39 en
dc.identifier.issue Supplement 2 en
dc.identifier.startpage W56 en
dc.identifier.endpage W60 en
dc.identifier.doi 10.1093/nar/gkr402
dc.neeo.contributor Davey|Norman E.|aut|
dc.neeo.contributor Haslam|Niall J.|aut|
dc.neeo.contributor Shields|Denis C.|aut|
dc.neeo.contributor Edwards|Richard J.|aut|
dc.description.othersponsorship BBSRC en
dc.description.admin ke,da,ti,SB-07/09/2011 en
dc.internal.rmsid 241502801


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