A multi-approaches-guided genetic algorithm with application to operon prediction.
OBJECTIVE
The prediction of operons is critical to the reconstruction of regulatory networks at the whole genome level. Multiple genome features have been used for predicting operons. However, multiple genome features are usually dealt with using only single method in the literatures. The aim of this paper is to develop a combined method for operon prediction by using different methods to preprocess different genome features in order for exerting their unique characteristics.


METHODS
A novel multi-approach-guided genetic algorithm for operon prediction is presented. We exploit different methods for intergenic distance, cluster of orthologous groups (COG) gene functions, metabolic pathway and microarray expression data. A novel local-entropy-minimization method is proposed to partition intergenic distance. Our program can be used for other newly sequenced genomes by transferring the knowledge that has been obtained from Escherichia coli data. We calculate the log-likelihood for COG gene functions and Pearson correlation coefficient for microarray expression data. The genetic algorithm is used for integrating the four types of data.


RESULTS
The proposed method is examined on E. coli K12 genome, Bacillus subtilis genome, and Pseudomonas aeruginosa PAO1 genome. The accuracies of prediction for these three genomes are 85.9987%, 88.296%, and 81.2384%, respectively.


CONCLUSIONS
Simulated experimental results demonstrate that in the genetic algorithm the preprocessing for genome data using multiple approaches ensures the effective utilization of different biological characteristics. Experimental results also show that the proposed method is applicable for predicting operons in prokaryote.
Wang
Shuqin
S
College of Computer Science and Technology, Jilin University, Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, Changchun 130012, China.
Wang
Yan
Y
Du
Wei
W
Sun
Fangxun
F
Wang
Xiumei
X
Zhou
Chunguang
C
Liang
Yanchun
Y
D000465:Algorithms; D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics; D008967:Molecular Biology / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D009876:Operon / Q000235:genetics*; D049490:Systems Biology / Q000379:methods*