Wormstep: An improved compact graphical representation of DNA sequences based on worm curve

Zhujin Zhang; Xiangxiang Zeng; Tao Song; Zhihua Chen; Xun Wang; Yunming Ye

doi:10.1166/jctn.2013.2677

Wormstep: An improved compact graphical representation of DNA sequences based on worm curve

Zhujin Zhang^*
, Xiangxiang Zeng
, Tao Song
, Zhihua Chen
, Xun Wang
, Yunming Ye

^*Corresponding author for this work

Harbin Institute of Technology Shenzhen
Xiamen University
Huazhong University of Science and Technology
University of Tsukuba

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

Abstract

Randic et al. proposed a famous compact graphical representation for visualizing and analyzing DNA sequences. However, it has a disadvantage that observers can not know the composition of DNA sequences except recoding the binary representation from start point. In this paper, we improve randic's model with a new representation-WormStep. WormStep has several advantages: (1) avoids degeneracy, (2) avoids loss of information, (3) highly compact, and (4) observers can immediately grasp the information about DNA base composition. Applications of WormStep on similarity analysis and phylogenetic tree study also are presented.

Original language	English
Pages (from-to)	189-193
Number of pages	5
Journal	Journal of Computational and Theoretical Nanoscience
Volume	10
Issue number	1
DOIs	https://doi.org/10.1166/jctn.2013.2677
State	Published - Jan 2013
Externally published	Yes

Keywords

Compact
Degeneracy
Graphical representation
Loss of information
Similarity analysis

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10.1166/jctn.2013.2677

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title = "Wormstep: An improved compact graphical representation of DNA sequences based on worm curve",

abstract = "Randic et al. proposed a famous compact graphical representation for visualizing and analyzing DNA sequences. However, it has a disadvantage that observers can not know the composition of DNA sequences except recoding the binary representation from start point. In this paper, we improve randic's model with a new representation-WormStep. WormStep has several advantages: (1) avoids degeneracy, (2) avoids loss of information, (3) highly compact, and (4) observers can immediately grasp the information about DNA base composition. Applications of WormStep on similarity analysis and phylogenetic tree study also are presented.",

keywords = "Compact, Degeneracy, Graphical representation, Loss of information, Similarity analysis",

author = "Zhujin Zhang and Xiangxiang Zeng and Tao Song and Zhihua Chen and Xun Wang and Yunming Ye",

year = "2013",

month = jan,

doi = "10.1166/jctn.2013.2677",

language = "英语",

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T2 - An improved compact graphical representation of DNA sequences based on worm curve

AU - Zhang, Zhujin

AU - Zeng, Xiangxiang

AU - Song, Tao

AU - Chen, Zhihua

AU - Wang, Xun

AU - Ye, Yunming

PY - 2013/1

Y1 - 2013/1

N2 - Randic et al. proposed a famous compact graphical representation for visualizing and analyzing DNA sequences. However, it has a disadvantage that observers can not know the composition of DNA sequences except recoding the binary representation from start point. In this paper, we improve randic's model with a new representation-WormStep. WormStep has several advantages: (1) avoids degeneracy, (2) avoids loss of information, (3) highly compact, and (4) observers can immediately grasp the information about DNA base composition. Applications of WormStep on similarity analysis and phylogenetic tree study also are presented.

AB - Randic et al. proposed a famous compact graphical representation for visualizing and analyzing DNA sequences. However, it has a disadvantage that observers can not know the composition of DNA sequences except recoding the binary representation from start point. In this paper, we improve randic's model with a new representation-WormStep. WormStep has several advantages: (1) avoids degeneracy, (2) avoids loss of information, (3) highly compact, and (4) observers can immediately grasp the information about DNA base composition. Applications of WormStep on similarity analysis and phylogenetic tree study also are presented.

KW - Compact

KW - Degeneracy

KW - Graphical representation

KW - Loss of information

KW - Similarity analysis

UR - https://www.scopus.com/pages/publications/84876573495

U2 - 10.1166/jctn.2013.2677

DO - 10.1166/jctn.2013.2677

M3 - 文章

AN - SCOPUS:84876573495

SN - 1546-1955

VL - 10

SP - 189

EP - 193

JO - Journal of Computational and Theoretical Nanoscience

JF - Journal of Computational and Theoretical Nanoscience

IS - 1

ER -

Wormstep: An improved compact graphical representation of DNA sequences based on worm curve

Abstract

Keywords

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