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 pre-defined 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 .
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References
Diella, F., Haslam, N., Chica, C., Budd, A., Michael, S., Brown, N.P., Trave, G., Gibson, T.J.: Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci. 13, 6580–6603 (2008)
Gould, C.M., Diella, F., Via, A., Puntervoll, P., Gemund, C., Chabanis-Davidson, S., Michael, S., Sayadi, A., Bryne, J.C., Chica, C., Seiler, M., Davey, N.E., Haslam, N., Weatheritt, R.J., Budd, A., Hughes, T., Pas, J., Rychlewski, L., Trave, G., Aasland, R., Helmer-Citterich, M., Linding, R., Gibson, T.J.: ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res. 38, D167–D180 (2010)
Kadaveru, K., Vyas, J., Schiller, M.R.: Viral infection and human disease–insights from minimotifs. Front Biosci. 13, 6455–6471 (2008)
Neduva, V., Russell, R.B.: Peptides mediating interaction networks: new leads at last. Curr. Opin. Biotechnol. 17, 465–471 (2006)
Rajasekaran, S., Balla, S., Gradie, P., Gryk, M.R., Kadaveru, K., Kundeti, V., Maciejewski, M.W., Mi, T., Rubino, N., Vyas, J., Schiller, M.R.: Minimotif miner 2nd release: a database and web system for motif search. Nucleic Acids Res. 37, D185–D190 (2009)
Ramu, C.: SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches. Nucleic Acids Res. 31, 3771–3774 (2003)
de Castro, E., Sigrist, C.J., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P.S., Gasteiger, E., Bairoch, A., Hulo, N.: ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res. 34, W362–W365 (2006)
Gutman, R., Berezin, C., Wollman, R., Rosenberg, Y., Ben-Tal, N.: QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns. Nucleic Acids Res. 33, W255–W261 (2005)
Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., Studholme, D.J., Yeats, C., Eddy, S.R.: The Pfam protein families database. Nucleic Acids Res. 32, D138–D141 (2004)
Sigrist, C.J., Cerutti, L., de Castro, E., Langendijk-Genevaux, P.S., Bulliard, V., Bairoch, A., Hulo, N.: PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res. 38, D161–D166 (2010)
Chica, C., Labarga, A., Gould, C.M., Lopez, R., Gibson, T.J.: A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. BMC Bioinformatics 9, 229 (2008)
Davey, N.E., Shields, D.C., Edwards, R.J.: Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinformatics 25, 443–450 (2009)
Via, A., Gould, C.M., Gemund, C., Gibson, T.J., Helmer-Citterich, M.: A structure filter for the Eukaryotic Linear Motif Resource. BMC Bioinformatics 10, 351 (2009)
Jonassen, I., Collins, J.F., Higgins, D.G.: Finding flexible patterns in unaligned protein sequences. Protein Sci. 4, 1587–1595 (1995)
Bailey, T.L., Boden, M., Buske, F.A., Frith, M., Grant, C.E., Clementi, L., Ren, J., Li, W.W., Noble, W.S.: MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–W208 (2009)
Neduva, V., Russell, R.B.: DILIMOT: discovery of linear motifs in proteins. Nucleic Acids Res. 34, W350–W355 (2006)
Davey, N.E., Shields, D.C., Edwards, R.J.: SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res. 34, 3546–3554 (2006)
Edwards, R.J., Davey, N.E., Shields, D.C.: SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins. PLoS ONE 2, e967 (2007)
Edwards, R.J., Davey, N.E., Shields, D.C.: CompariMotif: quick and easy comparisons of sequence motifs. Bioinformatics 24, 1307–1309 (2008)
Davey, N.E., Haslam, N.J., Shields, D.C., Edwards, R.J.: SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nucleic Acids Res. (2010)
Dosztanyi, Z., Csizmok, V., Tompa, P., Simon, I.: IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21, 3433–3434 (2005)
Bairoch, A., Apweiler, R., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., O’Donovan, C., Redaschi, N., Yeh, L.S.: The Universal Protein Resource (UniProt). Nucleic Acids Res. 33, D154–D159 (2005)
Davey, N.E., Edwards, R.J., Shields, D.C.: The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res. 35, W455–W459 (2007)
Russell, R.B., Gibson, T.J.: A careful disorderliness in the proteome: sites for interaction and targets for future therapies. FEBS Lett. 582, 1271–1275 (2008)
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997)
Neuwald, A.F., Green, P.: Detecting patterns in protein sequences. J. Mol. Biol. 239, 698–712 (1994)
Seiler, M., Mehrle, A., Poustka, A., Wiemann, S.: The 3of5 web application for complex and comprehensive pattern matching in protein sequences. BMC Bioinformatics 7, 144 (2006)
Lo, K.W., Naisbitt, S., Fan, J.S., Sheng, M., Zhang, M.: The 8-kDa dynein light chain binds to its targets via a conserved (K/R)XTQT motif. J. Biol. Chem. 276, 14059–14066 (2001)
Wellik, D.M.: Hox genes and vertebrate axial pattern. Curr. Top Dev. Biol. 88, 257–278 (2009)
Gehring, W.J., Affolter, M., Burglin, T.: Homeodomain proteins. Annu Rev. Biochem. 63, 487–526 (1994)
Sprules, T., Green, N., Featherstone, M., Gehring, K.: Lock and key binding of the HOX YPWM peptide to the PBX homeodomain. J. Biol. Chem. 278, 1053–1058 (2003)
Michael, S., Trave, G., Ramu, C., Chica, C., Gibson, T.J.: Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation. Bioinformatics 24, 453–457 (2008)
Hubbard, T.J., Aken, B.L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L., Coates, G., Fairley, S., Fitzgerald, S., Fernandez-Banet, J., Gordon, L., Graf, S., Haider, S., Hammond, M., Holland, R., Howe, K., Jenkinson, A., Johnson, N., Kahari, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Megy, K., Meidl, P., Overduin, B., Parker, A., Pritchard, B., Rios, D., Schuster, M., Slater, G., Smedley, D., Spooner, W., Spudich, G., Trevanion, S., Vilella, A., Vogel, J., White, S., Wilder, S., Zadissa, A., Birney, E., Cunningham, F., Curwen, V., Durbin, R., Fernandez-Suarez, X.M., Herrero, J., Kasprzyk, A., Proctor, G., Smith, J., Searle, S., Flicek, P.: Ensembl 2009. Nucleic Acids Res. 37, D690–D697 (2009)
Kersey, P.J., Lawson, D., Birney, E., Derwent, P.S., Haimel, M., Herrero, J., Keenan, S., Kerhornou, A., Koscielny, G., Kahari, A., Kinsella, R.J., Kulesha, E., Maheswari, U., Megy, K., Nuhn, M., Proctor, G., Staines, D., Valentin, F., Vilella, A.J., Yates, A.: Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res. 38, D563–D569 (2010)
Delpire, E., Gagnon, K.B.: Genome-wide analysis of SPAK/OSR1 binding motifs. Physiol Genomics 28, 223–231 (2007)
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Davey, N.E., Haslam, N.J., Shields, D.C., Edwards, R.J. (2010). SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context. In: Dijkstra, T.M.H., Tsivtsivadze, E., Marchiori, E., Heskes, T. (eds) Pattern Recognition in Bioinformatics. PRIB 2010. Lecture Notes in Computer Science(), vol 6282. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16001-1_5
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