[1] Xie Xueying, Sun Xiao, Lu Zuhong,. Auto-selection order of Markov chain forbackground sequences with chi-square test [J]. Journal of Southeast University (English Edition), 2003, 19 (4): 311-316. [doi:10.3969/j.issn.1003-7985.2003.04.002]

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Auto-selection order of Markov chain forbackground sequences with chi-square test()

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Journal of Southeast University (English Edition)[ISSN:1003-7985/CN:32-1325/N]

Volumn:

19

Issue:

2003 4

Page:

311-316

Research Field:

Biological Science and Medical Engineering

Publishing date:

2003-12-30

Info

Title:

Auto-selection order of Markov chain forbackground sequences with chi-square test

Author(s):

Xie Xueying;  Sun Xiao;  Lu Zuhong

Chien-Shiung Wu Laboratory, Southeast University, Nanjing 210096, China

Keywords:

non-coding sequences;  regulatory elements;  chi-square test;  Markov chain

PACS:

Q52

DOI:

10.3969/j.issn.1003-7985.2003.04.002

Abstract:

Modeling non-coding background sequences appropriately is important for the detection of regulatory elements from DNA sequences. Based on the chi-square statistic test, some explanations about why to choose higher-order Markov chain model and how to automatically select the proper order are given in this paper. The chi-square test is first run on synthetic data sets to show that it can efficiently find the proper order of Markov chain. Using chi-square test, distinct higher order context dependences inherent in ten sets of sequences of yeast S.cerevisiae from other literature have been found. So the Markov chain with higher-order would be more suitable for modeling the non-coding background sequences than an independent model.

References:

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Memo

Memo:

Biographies: Xie Xueying(1977—), female, graduate; Sun Xiao(corresponding author), male, doctor, professor, xsun@seu.edu.cn.

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