SLiMSearch: a webserver for finding novel occurrences of short linear motifs in proteins, incorporating sequence context


Davey, Norman E., Haslam, Niall J., Shields, Denis C. and Edwards, Richard J. (2010) SLiMSearch: a webserver for finding novel occurrences of short linear motifs in proteins, incorporating sequence context. In, Dijkstra, Tjeerd M.H., Tsivtsivadze, Evgeni, Marchiori, Elena and Heskes, Tom (eds.) Pattern Recognition in Bioinformatics. Second IAPR International Workshop (PRIB 2007) Heidelberg, DE, Springer, 50-61. (Lecture Notes in Computer Science, 6282). (doi:10.1007/978-3-642-16001-1).

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Description/Abstract

Short, linear motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch (Short, Linear Motif Search) webserver is a flexible tool that enables researchers to identify novel occurrences of predefined SLiMs in sets of proteins. Numerous masking options give the user great control over the contextual information to be included in the analyses, including evolutionary filtering and protein structural disorder. User-friendly output and visualizations of motif context allow the user to quickly gain insight into the validity of a putatively functional motif occurrence. Users can search motifs against the human proteome, or submit their own datasets of UniProt proteins, in which case motif support within the dataset is statistically assessed for over- and under-representation, accounting for evolutionary relationships between input proteins. SLiMSearch is freely available as open source Python modules and all webserver results are available for download. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch.html

Item Type: Book Section
Subjects: Q Science > QA Mathematics > QA76 Computer software
Divisions: University Structure - Pre August 2011 > School of Biological Sciences
ePrint ID: 166213
Date Deposited: 26 Oct 2010 08:00
Last Modified: 27 Mar 2014 19:18
Publisher: Springer
URI: http://eprints.soton.ac.uk/id/eprint/166213

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