Chapter 12. Neighborhood Profile Search for Motif Refinement

  1. Yan-Qing Zhang3 and
  2. Jagath C. Rajapakse4
  1. Chandan K. Reddy1,
  2. Yao-Chung Weng2 and
  3. Hsiao-Dong Chiang2

Published Online: 21 APR 2008

DOI: 10.1002/9780470397428.ch12

Machine Learning in Bioinformatics

Machine Learning in Bioinformatics

How to Cite

Reddy, C. K., Weng, Y.-C. and Chiang, H.-D. (2008) Neighborhood Profile Search for Motif Refinement, in Machine Learning in Bioinformatics (eds Y.-Q. Zhang and J. C. Rajapakse), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470397428.ch12

Editor Information

  1. 3

    Georgia State University, Atlanta, Georgia

  2. 4

    School of Computer Engineering, and The Bioinformatics Research Center, Nanyang Technological University, Nanyang, Singapore

Author Information

  1. 1

    Wayne State University, Detroit, Michigan, USA

  2. 2

    Cornell University, Ithaca, New York, USA

Publication History

  1. Published Online: 21 APR 2008
  2. Published Print: 12 NOV 2008

Book Series:

  1. Bioinformatics: Computational Techniques and Engineering

Book Series Editors:

  1. Professor Yi Pan and
  2. Professor Albert Y. Zomaya

ISBN Information

Print ISBN: 9780470116623

Online ISBN: 9780470397428



  • neighborhood profile search for motif refinement;
  • new computational approach in finding regulatory sites in efficient manner;
  • TT-EM methodology for real biological sequences


This chapter contains sections titled:

  • Introduction

  • Relevant Background

  • Profile Model and the EM Algorithm

  • Novel Framework

  • Implementation Details

  • Experimental Results

  • Concluding Discussion

  • References