DocumentCode :
2460518
Title :
Particle Swarm Optimization with Extremal Optimization for the Prediction of CpG Islands in the Mammal Genome
Author :
Chuang, Li-Yeh ; Lin, Ming-Cheng ; Yang, Cheng-Hong
Author_Institution :
Dept. of Chem. Eng., I-Shou Univ., Kaohsiung, Taiwan
fYear :
2011
fDate :
24-26 Oct. 2011
Firstpage :
189
Lastpage :
194
Abstract :
Regions with abundant GC nucleotides in a genome, which are often referred to as CpG islands, have been used in methylation analysis and the prediction of promoter regions. In this study, we propose PSOEO (Particle Swarm Optimization with Extremal Optimization), a method for the prediction of CpG islands in the mammal genome. This method adopts the GGF criteria (GC content ≥ 50%, observed/expected (O/E) ratio ≥0.6 and length ≥200 bp) for the search of CpG islands. First, we used the PSO algorithm to predict CpG islands. In a second stage, we used EO to search for various output states (local search) in order to find a better result. Extremal optimization is a developed heuristic local search method. Finally, we used five evaluation criteria, namely the sensitivity (SN), specificity (SP), accuracy (ACC), correlation coefficient (CC) and performance coefficient (PC) to compare other methods in the literature. PSOEO method provided better SN and CC predictions for the locations of CpG islands than the other methods it was compared to.
Keywords :
DNA; genomics; molecular biophysics; particle swarm optimisation; CpG islands; GGF criteria; abundant GC nucleotides; correlation coefficient; extremal optimization; heuristic local-search method; mammal genome; methylation analysis; particle swarm optimization; performance coefficient; promoter region prediction; Bioinformatics; Educational institutions; Genomics; Optimization; Particle swarm optimization; Prediction algorithms; Tin; CpG islands; Extremal Optimization; Particle Swarm Optimization;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Bioinformatics and Bioengineering (BIBE), 2011 IEEE 11th International Conference on
Conference_Location :
Taichung
Print_ISBN :
978-1-61284-975-1
Type :
conf
DOI :
10.1109/BIBE.2011.36
Filename :
6089827
Link To Document :
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