A hybrid algorithm based on artificial immune system and hidden Markov model for multiple sequence alignment

被引：1
作者：
Ge, Hongwei [1 ]
Zhong, Weimin [1 ]
Du, Wenli [1 ]
Qian, Feng [1 ]
Wang, Lu
机构：
[1] E China Univ Sci & Technol, Automat Inst, State Key Lab Chem Engn, Shanghai 200237, Peoples R China
来源：
PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS AND KNOWLEDGE ENGINEERING (ISKE 2007) | 2007年
关键词：
artificial immune system; hidden Markov model; multiple sequence alignment;
D O I：
10.2991/iske.2007.162
中图分类号：
TP18 [人工智能理论];
学科分类号：
081104 ; 0812 ; 0835 ; 1405 ;
摘要：
Multiple sequence alignment (MSA) has become an essential tool in the analysis of biologic sequences. In this paper, an artificial immune system (AIS) is proposed to train hidden Markov models (HMMs). Further, an integration algorithm based on the HMM and AIS for the MSA is constructed and a decoding algorithm based on Viterbi algorithm is also proposed. The approach is tested on a set of standard instances taken from the benchmark alignment database, BAliBASE. Numerical results are compared with those obtained by using the Baum-Welch training algorithm. The results show that the proposed algorithm not only improves the alignment abilities, but also reduces the time cost.
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相关论文
共 16 条
[1]  
Andrews PS, 2005, LECT NOTES COMPUT SC, V3627, P126
[2]   Solving job shop scheduling problems using artificial immune system [J].
Chandrasekaran, M. ;
Asokan, P. ;
Kumanan, S. ;
Balamurugan, T. ;
Nickolas, S. .
INTERNATIONAL JOURNAL OF ADVANCED MANUFACTURING TECHNOLOGY, 2006, 31 (5-6) :580-593
[3]   Hidden Markov models for the burst error statistics of Viterbi decoding [J].
Chao, CC ;
Yao, YL .
IEEE TRANSACTIONS ON COMMUNICATIONS, 1996, 44 (12) :1620-1622
[4]  
Du ZH, 2004, LECT NOTES ARTIF INT, V3066, P792
[5]   SATCHMO:: sequence alignment and tree construction using hidden Markov models [J].
Edgar, RC ;
Sjölander, K .
BIOINFORMATICS, 2003, 19 (11) :1404-1411
[6]  
GOTOH O, 1993, COMPUT APPL BIOSCI, V9, P361
[7]  
Li ZH, 2006, LECT NOTES ARTIF INT, V4251, P153
[8]  
Otterpohl JR, 2002, LECT NOTES COMPUT SC, V2415, P1180
[9]  
SAHA, 2007, COMPUTERS BIOL MED, V37, P415
[10]  
Shyu C, 2003, LECT NOTES COMPUT SC, V2724, P2313
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