« Previous Abstract[Allelopathy of invasive weeds: a simulation study with cellular automata model]    Next AbstractDetermination of four heterocyclic insecticides by ionic liquid dispersive liquid-liquid microextraction in water samples »

BMC Genomics

Title:		Artificial ants deposit pheromone to search for regulatory DNA elements
Author(s):		Liu Y; Yokota H;
Address:		"Division of Biostatistics, Department of Medicine, Center for Computational Biology and Bioinformatics, Indiana University--Purdue University Indianapolis, Indianapolis, IN 46202, USA. yunliu@iupui.edu"
Journal Title:		BMC Genomics
Year:		2006
Volume:		20060830
Issue:
Page Number:		221 -
DOI:		10.1186/1471-2164-7-221
ISSN/ISBN:		1471-2164 (Electronic) 1471-2164 (Linking)
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, NFkappaB, 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"
Keywords:		"5' Untranslated Regions/genetics Algorithms Animals Ants/*genetics Chondrogenesis/genetics DNA/*genetics Gene Expression Regulation Humans Models, Genetic Pheromones/*genetics Regulatory Sequences, Nucleic Acid Reproducibility of Results;"
Notes:		"MedlineLiu, Yunlong Yokota, Hiroki eng R01 AR050008/AR/NIAMS NIH HHS/ R01 AR50008/AR/NIAMS NIH HHS/ Research Support, N.I.H., Extramural England 2006/09/01 BMC Genomics. 2006 Aug 30; 7:221. doi: 10.1186/1471-2164-7-221"