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. 2011 Sep:Chapter 13:13.15.1-13.15.24.
doi: 10.1002/0471250953.bi1315s35.

Biological sequence motif discovery using motif-x

Michael F Chou  1 , Daniel Schwartz  2
Affiliations

Biological sequence motif discovery using motif-x

Michael F Chou et al. Curr Protoc Bioinformatics. 2011 Sep.

Abstract

The Web-based motif-x program provides a simple interface to extract statistically significant motifs from large data sets, such as MS/MS post-translational modification data and groups of proteins that share a common biological function. Users upload data files and download results using common Web browsers on essentially any Web-compatible computer. Once submitted, data analyses are performed rapidly on an associated high-speed computer cluster and they produce both syntactic and image-based motif results and statistics. The protocols presented demonstrate the use of motif-x in three common user scenarios.

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References

Literature Cited

References
    1. Bonferroni, C.E. 1935. Il calcolo delle assicurazioni su gruppi di teste. In Studi in Onore del Professore Salvatore Ortu Carboni. 13-60.
    1. Chou, M.F. and Schwartz, D. 2011. Using the scan-X web site to predict protein post-translational modifications. Curr. Protocol. Bioinform. Submitted.
    1. Dinkel, H., Chica, C., Via, A., Gould, C.M., Jensen, L.J., Gibson, T.J., and Diella, F. 2011. Phospho.ELM: A database of phosphorylation sites-update 2011. Nucleic Acids Res. 39:D261-D267.
    1. Durek, P., Schmidt, R., Heazlewood, J.L., Jones, A., MacLean, D., Nagel, A., Kersten, B., and Schulze, W.X. 2010. PhosPhAt: The Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Res. 38:D828-D834.
    1. Edwards, R.J., Davey, N.E., and Shields, D.C. 2008. CompariMotif: Quick and easy comparisons of sequence motifs. Bioinformatics 24:1307-1309.
Key Reference
    1. Schwartz and Gygi, . See above.
Internet Resources
    1. http://motif-x.med.harvard.edu
Supplemental Data Files
    1. File 1
    1. File 2
    1. File 3
    1. File 4

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