Artificial ants deposit pheromone to search for regulatory DNA elements

Yunlong Liu, Hiroki Yokota

Research output: Contribution to journalArticle

6 Scopus citations

Abstract

Background: Identification of transcription-factor binding motifs (DNA sequences) can be formulated as a combinatorial problem, where an efficient algorithm is indispensable to predict the role of multiple binding motifs. An ant algorithm is a biology-inspired computational technique, through which a combinatorial problem is solved by mimicking the behavior of social insects such as ants. We developed a unique version of ant algorithms to select a set of binding motifs by considering a potential contribution of each of all random DNA sequences of 4- to 7-bp in length. Results: Human chondrogenesis was used as a model system. The results revealed that the ant algorithm was able to identify biologically known binding motifs in chondrogenesis such as AP-1, NFκB, and sox9. Some of the predicted motifs were identical to those previously derived with the genetic algorithm. Unlike the genetic algorithm, however, the ant algorithm was able to evaluate a contribution of individual binding motifs as a spectrum of distributed information and predict core consensus motifs from a wider DNA pool. Conclusion: The ant algorithm offers an efficient, reproducible procedure to predict a role of individual transcription-factor binding motifs using a unique definition of artificial ants.

Original languageEnglish (US)
Article number221
JournalBMC genomics
Volume7
DOIs
StatePublished - Aug 30 2006

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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