An effective algorithm of motif finding problem

Yong Chen, Guojun Li

Research output: Contribution to journalArticlepeer-review


Identification of the short DNA sequence motif, which serves as binding targets for transcription factors, is a fundamental problem in both computer science and molecular biology. Especially, finding the subtle motifs with variable gaps is more challenging. In this paper, a new algorithm is presented, which explores some new strategies. • Based on a neighbourhood set concept, a new probability matrix is defined, which can capture the target motifs effectively. • An iterative restart strategy is used, by which we can use several similar motifs' information to detect the real motif to demonstrate the effectiveness of our algorithm. We test it on several kinds of data and compare it with some other current representation algorithms. Simulation shows that the algorithm can effectively detect the subtle motifs.

Original languageEnglish (US)
Pages (from-to)137-149
Number of pages13
JournalInternational Journal of Bioinformatics Research and Applications
Issue number2
StatePublished - May 2008
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Health Informatics
  • Clinical Biochemistry
  • Health Information Management


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