SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs - PubMed (original) (raw)

. 2010 Jul;38(Web Server issue):W534-9.

doi: 10.1093/nar/gkq440. Epub 2010 May 23.

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

Norman E Davey et al. Nucleic Acids Res. 2010 Jul.

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.

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Figures

Figure 1.

Figure 1.

Input options. Options are separated into sequence masking, SLiMBuild motif construction and SLiMChance/Output filtering. For clarity, all options correspond to commandline parameters of downloadable SLiMFinder program; short descriptions and commandline parameter names are given if the mouse hovers over the help buttons. All options are described in the help pages. Once options have been set/reviewed, ‘Submit job’ will move the job into the run queue.

Figure 2.

Figure 2.

Main results page. Summarized results for each motif are initially displayed. These can be expanded to reveal individual occurrences in each protein for each motif. Alignments can be generated to explore the unmasked and masked sequence context for each motif ‘(M|A)’ or to examine the region around a specific motif occurrence in a single protein ‘(Plot)’. All visualizations can be exported as PNGs or high-quality PDFs.

Figure 3.

Figure 3.

CompariMotif results. All motifs returned by SLiMFinder are cross-referenced against known motifs using CompariMotif, enabling easy identification of re-discovered known motifs. All columns are sortable by clicking on their respective headings and more information can be revealed about motifs and their CompariMotif hits by mousing over the appropriate data.

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