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Front. Inform. Technol. Electron. Eng.  2011, Vol. 12 Issue (4): 263-272    DOI: 10.1631/jzus.C1000091
    
Structural visualization of sequential DNA data
Xiao-hong Mao1, Jing-hua Fu2, Wei Chen*,2, Qian You3, Shiao-fen Fang3, Qun-sheng Peng2
1 The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310013, China 2 State Key Lab of CAD & CG, Zhejiang University, Hangzhou 310058, China 3 Department of Computer and Information Science, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, IN 46202, USA
Structural visualization of sequential DNA data
Xiao-hong Mao1, Jing-hua Fu2, Wei Chen*,2, Qian You3, Shiao-fen Fang3, Qun-sheng Peng2
1 The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310013, China 2 State Key Lab of CAD & CG, Zhejiang University, Hangzhou 310058, China 3 Department of Computer and Information Science, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, IN 46202, USA
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摘要： To date, comparing and visualizing genome sequences remain challenging due to the large genome size. Existing approaches take advantage of the stable property of oligonucleotides and exhibit the main characteristics of the whole genome, yet they commonly fail to show progression patterns of the genome adjustably. This paper presents a novel visual encoding technique, which not only supports the binning process (phylogenetic analysis), but also allows the sequential analysis of the genome. The key idea is to regard the combination of each k-nucleotide and its reverse complement as a visual word, and to represent a long genome sequence with a list of local statistical feature vectors derived from the local frequency of the visual words. Experimental results on a variety of examples demonstrate that the presented approach has the ability to quickly and intuitively visualize DNA sequences, and to help the user identify regions of differences among multiple datasets.
关键词： Genome sequence;  Sequential visualization;  Bio-information visualization    
Abstract: To date, comparing and visualizing genome sequences remain challenging due to the large genome size. Existing approaches take advantage of the stable property of oligonucleotides and exhibit the main characteristics of the whole genome, yet they commonly fail to show progression patterns of the genome adjustably. This paper presents a novel visual encoding technique, which not only supports the binning process (phylogenetic analysis), but also allows the sequential analysis of the genome. The key idea is to regard the combination of each k-nucleotide and its reverse complement as a visual word, and to represent a long genome sequence with a list of local statistical feature vectors derived from the local frequency of the visual words. Experimental results on a variety of examples demonstrate that the presented approach has the ability to quickly and intuitively visualize DNA sequences, and to help the user identify regions of differences among multiple datasets.
Key words: Genome sequence    Sequential visualization    Bio-information visualization
收稿日期: 2010-04-11 出版日期: 2011-04-11
CLC:  TP391.1  
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Xiao-hong Mao
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Shiao-fen Fang
Qun-sheng Peng

引用本文:

Xiao-hong Mao, Jing-hua Fu, Wei Chen, Qian You, Shiao-fen Fang, Qun-sheng Peng. Structural visualization of sequential DNA data. Front. Inform. Technol. Electron. Eng., 2011, 12(4): 263-272.

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http://www.zjujournals.com/xueshu/fitee/CN/10.1631/jzus.C1000091    或    http://www.zjujournals.com/xueshu/fitee/CN/Y2011/V12/I4/263

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