Methodology article
Artificial ants deposit pheromone to search for regulatory DNA elements
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* Corresponding author: Yunlong Liu yunliu@iupui.edu
1 Division of Biostatistics, Department of Medicine, Center for Computational Biology and Bioinformatics, Indiana University – Purdue University Indianapolis, Indianapolis, IN 46202, USA
2 Department of Biomedical Engineering, Indiana University – Purdue University Indianapolis, Indianapolis, IN 46202, USA
BMC Genomics 2006, 7:221 doi:10.1186/1471-2164-7-221
Published: 30 August 2006Abstract
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.