SLiMFinder : a web server to find novel, significantly over-represented, short protein motifs

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Title: SLiMFinder : a web server to find novel, significantly over-represented, short protein motifs
Authors: Davey, Norman E.
Haslam, Niall J.
Shields, Denis C.
Edwards, Richard J.
Permanent link: http://hdl.handle.net/10197/2561
Date: Jul-2010
Abstract: Short, linear motifs (SLiMs) play a critical role in many biological processes, particularly in protein–protein interactions. The Short, Linear Motif Finder (SLiMFinder) web server is a de novo motif discovery tool that identifies statistically over-represented motifs in a set of protein sequences, accounting for the evolutionary relationships between them. Motifs are returned with an intuitive P-value that greatly reduces the problem of false positives and is accessible to biologists of all disciplines. Input can be uploaded by the user or extracted directly from UniProt. Numerous masking options give the user great control over the contextual information to be included in the analyses. The SLiMFinder server combines these with user-friendly output and visualizations of motif context to allow the user to quickly gain insight into the validity of a putatively functional motif. These visualizations include alignments of motif occurrences, alignments of motifs and their homologues and a visual schematic of the top-ranked motifs. Returned motifs can also be compared with known SLiMs from the literature using CompariMotif. All results are available for download. The SLiMFinder server is available at: http://bioware.ucd.ie/slimfinder.html.
Funding Details: Science Foundation Ireland
European Research Council
Other funder
Type of material: Journal Article
Publisher: Oxford University Press
Copyright (published version): 2010 The Author(s)
Keywords: Linear motif;Protein-protein interaction
Subject LCSH: Protein-protein interactions
Proteins--Research--Data processing
Proteins--Research--Technological innovations
DOI: 10.1093/nar/gkq440
Language: en
Status of Item: Peer reviewed
Appears in Collections:Conway Institute Research Collection
CASL Research Collection

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