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Using Markov model to improve word normalization algorithm for biological sequence comparison

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Abstract

There are two crucial problems with statistical measures for sequence comparison: overlapping structures and background information of words in biological sequences. Word normalization in improved composition vector method took into account these problems and achieved better performance in evolutionary analysis. The word normalization is desirable, but not sufficient, because it assumes that the four bases A, C, T, and G occur randomly with equal chance. This paper proposed an improved word normalization which uses Markov model to estimate exact k-word distribution according to observed biological sequence and thus has the ability to adjust the background information of the k-word frequencies in biological sequences. The improved word normalization was tested with three experiments and compared with the existing word normalization. The experiment results confirm that the improved word normalization using Markov model to estimate the exact k-word distribution in biological sequences is more efficient.

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Acknowledgments

The author thanks all the anonymous referees for their valuable suggestions and support. This work is supported by the National Natural Science Foundation of China (61001214, 61003191), and a research grants (Y2100930, Y6100339) from Zhejiang Provincial Natural Science Foundation of China.

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Authors and Affiliations

  1. College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, People’s Republic of China

    Qi Dai, Yuhua Yao & Fukun Zhao

  2. School of Science, Hangzhou Dianzi University, Hangzhou, 310018, People’s Republic of China

    Xiaoqing Liu

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  1. Qi Dai
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  2. Xiaoqing Liu
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  3. Yuhua Yao
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  4. Fukun Zhao
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Correspondence to Qi Dai.

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Dai, Q., Liu, X., Yao, Y. et al. Using Markov model to improve word normalization algorithm for biological sequence comparison. Amino Acids 42, 1867–1877 (2012). https://doi.org/10.1007/s00726-011-0906-2

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