Article

Acta Biochim Biophys Sin 2005,37:435-439

doi:10.1111/j.1745-7270.2005.00065.x

Recognition of Gene Acceptor Site Based on Multi-objective Optimization

Jing ZHAO1,3,4, Yue-Min ZHU2, Pei-Ming SONG1, Qing FANG1, and Jian-Hua LUO1,3*

1 School of Life Science & Technology, Shanghai Jiaotong University, Shanghai 200240, China;

2 CREATIS, CNRS UMR 5515, INSA Lyon, 69621 Villeurbanne Cedex, France;

3 Shanghai Center for Bioinformation and Technology, Shanghai 200235, China;

4 Logistical Engineering University, Chongqing 400016, China

Abstract A new method for predicting the gene acceptor site based on multi-objective optimization is introduced in this paper. The models for the acceptor, branch and distance between acceptor site and branch site were constructed according to the characteristics of the sequences from the exon-intron database and using common biological knowledge. The acceptor function, branch function and distance function were defined respectively, and the multi-objective optimization model was constructed to recognize the splice site. The test results show that the algorithm used in this study performs better than the SplicePredictor, which is one of the leading acceptor site detectors.

Key words multi-objective optimization; acceptor site; recognition

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