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


Davey, Norman E., Haslam, Niall J., Shields, Denis C. and Edwards, Richard J. (2010) SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nucleic Acids Research (doi:10.1093/nar/gkq440).

Download

Full text not available from this repository.

Description/Abstract

Short, linear motifs (SLiMs) play a critical role in many biological processes, particularly in protein–protein interactions. The SLiMFinder (Short, Linear Motif Finder) 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 visualisations of motif context to allow the user to quickly gain insight into the validity of a putatively functional motif. These visualisations 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 to 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.

Item Type: Article
ISSNs: 0305-1048 (print)
1362-4962 (electronic)
Subjects: Q Science > Q Science (General)
Divisions: University Structure - Pre August 2011 > School of Biological Sciences
ePrint ID: 154463
Date Deposited: 25 May 2010 10:31
Last Modified: 27 Mar 2014 19:12
URI: http://eprints.soton.ac.uk/id/eprint/154463

Actions (login required)

View Item View Item