SLiMSearch 2.0: biological context for short linear motifs in proteins


Davey, Norman E., Haslam, Niall J., Shields, Denis C. and Edwards, Richard J (2011) SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Research, 39, (S2), W56-W60. (doi:10.1093/nar/gkr402 ). (PMID:21622654).

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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.

Item Type: Article
ISSNs: 0305-1048 (print)
1362-4962 (electronic)
Subjects: Q Science > QH Natural history > QH301 Biology
R Medicine > R Medicine (General)
Divisions: University Structure - Pre August 2011 > School of Biological Sciences
ePrint ID: 189719
Date Deposited: 06 Jun 2011 12:33
Last Modified: 27 Mar 2014 19:42
URI: http://eprints.soton.ac.uk/id/eprint/189719

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