Proceedings of the 2007 International Conference on Intelligent Systems and Knowledge Engineering (ISKE 2007)

A Hybrid Algorithm Based on Artificial Immune System and Hidden Markov Model for Multiple Sequence Alignment

Authors
Hongwei Ge1, Weimin Zhong, Wenli Du, Feng Qian, Lu Wang
1Automation Institute, East China University of Science and Technology, State-Key Laboratory of Chemical Engineering
Corresponding Author
Hongwei Ge
Available Online October 2007.
DOI
https://doi.org/10.2991/iske.2007.162How to use a DOI?
Keywords
Artificial immune system, hidden Markov model, multiple sequence alignment
Abstract

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.

Copyright
© 2007, the Authors. Published by Atlantis Press.
Open Access
This is an open access article distributed under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/).

Download article (PDF)

Volume Title
Proceedings of the 2007 International Conference on Intelligent Systems and Knowledge Engineering (ISKE 2007)
Series
Advances in Intelligent Systems Research
Publication Date
October 2007
ISBN
978-90-78677-04-8
ISSN
1951-6851
DOI
https://doi.org/10.2991/iske.2007.162How to use a DOI?
Copyright
© 2007, the Authors. Published by Atlantis Press.
Open Access
This is an open access article distributed under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/).

Cite this article

TY  - CONF
AU  - Hongwei Ge
AU  - Weimin Zhong
AU  - Wenli Du
AU  - Feng Qian
AU  - Lu Wang
PY  - 2007/10
DA  - 2007/10
TI  - A Hybrid Algorithm Based on Artificial Immune System and Hidden Markov Model for Multiple Sequence Alignment
BT  - Proceedings of the 2007 International Conference on Intelligent Systems and Knowledge Engineering (ISKE 2007)
PB  - Atlantis Press
SP  - 952
EP  - 958
SN  - 1951-6851
UR  - https://doi.org/10.2991/iske.2007.162
DO  - https://doi.org/10.2991/iske.2007.162
ID  - Ge2007/10
ER  -