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Identifying CpG Islands in Genome Using Conditional Random Fields

  • Wei Liu
  • Hanwu Chen
  • Ling Chen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7389)

Abstract

This paper presents a novel method for CpG islands location identification based on conditional random fields (CRF) model. The method transforms CpG islands location identification into the problem of sequential data labeling. Based on the nature of CpG islands location, we design the methods of model constructing, training and decoding in CRF accordingly. Experimental results on benchmark data sets show that our algorithm is more practicable and efficient than the traditional methods.

Keywords

conditional random fields model CpG islands sequential data labeling 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Wei Liu
    • 1
    • 2
  • Hanwu Chen
    • 1
  • Ling Chen
    • 2
    • 3
  1. 1.Department of Computer Science and EngineeringSoutheast UniversityNanjingChina
  2. 2.Department of Computer ScienceYangzhou UniversityYangzhouChina
  3. 3.National Key Lab of Novel Software TechNanjing UniversityNanjingChina

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