Nucleic Acids Research Advance Access originally published online on June 18, 2007
Nucleic Acids Research 2007 35(Web Server issue):W455-W459; doi:10.1093/nar/gkm400
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W455-W459
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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The SLiMDisc server: short, linear motif discovery in proteins
UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
*To whom correspondence should be addressed. Tel: +353-1-7165344; Fax: +353-1-7166701; Email: denis.shields{at}ucd.ie
Received January 29, 2007. Revised April 30, 2007. Accepted May 1, 2007.
Short, linear motifs (SLiMs) play a critical role in many biological processes, particularly in protein–protein interactions. Overrepresentation of convergent occurrences of motifs in proteins with a common attribute (such as similar subcellular location or a shared interaction partner) provides a feasible means to discover novel occurrences computationally. The SLiMDisc (Short, Linear Motif Discovery) web server corrects for common ancestry in describing shared motifs, concentrating on the convergently evolved motifs. The server returns a listing of the most interesting motifs found within unmasked regions, ranked according to an information content-based scoring scheme. It allows interactive input masking, according to various criteria. Scoring allows for evolutionary relationships in the data sets through treatment of BLAST local alignments. Alongside this ranked list, visualizations of the results improve understanding of the context of suggested motifs, helping to identify true motifs of interest. These visualizations include alignments of motif occurrences, alignments of motifs and their homologues and a visual schematic of the top-ranked motifs. Additional options for filtering and/or re-ranking motifs further permit the user to focus on motifs with desired attributes. Returned motifs can also be compared with known SLiMs from the literature. SLiMDisc is available at: http://bioware.ucd.ie/~slimdisc/.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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  R. J. Edwards, N. E. Davey, and D. C. Shields CompariMotif: quick and easy comparisons of sequence motifs Bioinformatics, May 15, 2008; 24(10): 1307 - 1309. [Abstract] [Full Text] [PDF]
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