UNIT 13.15 Biological Sequence Motif Discovery Using motif-x

  1. Michael F. Chou1,
  2. Daniel Schwartz2

Published Online: 1 SEP 2011

DOI: 10.1002/0471250953.bi1315s35

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Chou, M. F. and Schwartz, D. 2011. Biological Sequence Motif Discovery Using motif-x. Current Protocols in Bioinformatics. 35:13.15:13.15.1–13.15.24.

Author Information

  1. 1

    Department of Genetics, Harvard Medical School, Boston, Massachusetts

  2. 2

    Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut

Publication History

  1. Published Online: 1 SEP 2011
  2. Published Print: SEP 2011


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. Curr. Protoc. Bioinform. 35:13.15.1-13.15.24. © 2011 by John Wiley & Sons, Inc.


  • protein motif;
  • phosphorylation;
  • post-translational modification (PTM);
  • motif discovery;
  • motif-x;
  • mass spectrometry;
  • proteomics