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J Theor Biol. 2013 Nov 7;336:52-60. doi: 10.1016/j.jtbi.2013.07.008. Epub 2013 Jul 19.

Study of LZ-word distribution and its application for sequence comparison.

Author information

  • 1College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China. Electronic address: daiailiu2004@yahoo.com.cn.

Abstract

Lempel-Ziv complexity has been widely used for sequence comparison and achieved promising results, but until now components' distribution in exhaustive history has not been studied. This paper investigated the whole distribution of LZ-words and presented a novel statistical method for sequence comparison. With the components' length in mind, we revised Lempel-Ziv complexity and obtained various sets of LZ-words. Instead of calculating the LZ-words' contents, we defined a series of set operations on LZ-word set to compare biological sequences. In order to assess the effectiveness of the proposed method, we performed two sets of experiments and compared it with alignment-based methods.

Copyright © 2013 Elsevier Ltd. All rights reserved.

KEYWORDS:

Lempel–Ziv complexity; Phylogenetic analysis; Set operation; Word set

PMID:
23876763
[PubMed - in process]
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