An improved heuristic algorithm for finding motif signals in DNA sequences

Chao Wen Huang, Wun Shiun Lee, Sun Yuan Hsieh

Research output: Contribution to journalArticlepeer-review

27 Citations (Scopus)

Abstract

The planted (l,d)-motif search problem is a mathematical abstraction of the DNA functional site discovery task. In this paper, we propose a heuristic algorithm that can find planted (l,d)-signals in a given set of DNA sequences. Evaluations on simulated data sets demonstrate that the proposed algorithm outperforms current widely used motif finding algorithms. We also report the results of experiments on real biological data sets.

Original languageEnglish
Article number5582077
Pages (from-to)959-975
Number of pages17
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume8
Issue number4
DOIs
Publication statusPublished - 2011

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics
  • Applied Mathematics

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