Study of inter-sequence similarity for multiple DNA sequence compression

Paula Wu; Ngai Fong Law; W. C. Siu

doi:10.1063/1.2816620

Study of inter-sequence similarity for multiple DNA sequence compression

Paula Wu, Ngai Fong Law, W. C. Siu

The Hong Kong Polytechnic University

Research output: Chapter in book / Conference proceeding › Conference article published in proceeding or book › Academic research › peer-review

Abstract

Current DNA compression algorithms rely on finding repetitions within the DNA sequence so that similar subsequences can be encoded by referencing to each other. In this paper, we explore similarities between different chromosomes of the sequence "Saccharomyces cerevisiae". These similarities are characterized by the existence of similar subsequences among different chromosomes. The longer the similar subsequences are, the higher the cross-similarities are. Our study indicates that these cross-sequence similarities are often significant as compared to self-sequence similarities. This implies that it would be advantageous to compress two or more sequences together so that similar subsequences found between multiple sequences can be encoded together.

Original language	English
Title of host publication	Computational Models For Life Sciences (CMLS '07) - 2007 International Symposium
Pages	167-176
Number of pages	10
Volume	952
DOIs	https://doi.org/10.1063/1.2816620
Publication status	Published - 1 Dec 2007
Event	2007 International Symposium on Computational Models for Life Sciences, CMLS '07 - Gold Coast, QLD, Australia Duration: 17 Dec 2007 → 19 Dec 2007

Conference

Conference	2007 International Symposium on Computational Models for Life Sciences, CMLS '07
Country/Territory	Australia
City	Gold Coast, QLD
Period	17/12/07 → 19/12/07

Keywords

DNA compression
DNA sequence similarity

ASJC Scopus subject areas

General Physics and Astronomy

More information

10.1063/1.2816620

Cite this

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title = "Study of inter-sequence similarity for multiple DNA sequence compression",

abstract = "Current DNA compression algorithms rely on finding repetitions within the DNA sequence so that similar subsequences can be encoded by referencing to each other. In this paper, we explore similarities between different chromosomes of the sequence {"}Saccharomyces cerevisiae{"}. These similarities are characterized by the existence of similar subsequences among different chromosomes. The longer the similar subsequences are, the higher the cross-similarities are. Our study indicates that these cross-sequence similarities are often significant as compared to self-sequence similarities. This implies that it would be advantageous to compress two or more sequences together so that similar subsequences found between multiple sequences can be encoded together.",

keywords = "DNA compression, DNA sequence similarity",

author = "Paula Wu and Law, {Ngai Fong} and Siu, {W. C.}",

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Study of inter-sequence similarity for multiple DNA sequence compression. / Wu, Paula; Law, Ngai Fong; Siu, W. C.
Computational Models For Life Sciences (CMLS '07) - 2007 International Symposium. Vol. 952 2007. p. 167-176.

Research output: Chapter in book / Conference proceeding › Conference article published in proceeding or book › Academic research › peer-review

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AB - Current DNA compression algorithms rely on finding repetitions within the DNA sequence so that similar subsequences can be encoded by referencing to each other. In this paper, we explore similarities between different chromosomes of the sequence "Saccharomyces cerevisiae". These similarities are characterized by the existence of similar subsequences among different chromosomes. The longer the similar subsequences are, the higher the cross-similarities are. Our study indicates that these cross-sequence similarities are often significant as compared to self-sequence similarities. This implies that it would be advantageous to compress two or more sequences together so that similar subsequences found between multiple sequences can be encoded together.

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M3 - Conference article published in proceeding or book

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BT - Computational Models For Life Sciences (CMLS '07) - 2007 International Symposium

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Study of inter-sequence similarity for multiple DNA sequence compression

Abstract

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Keywords

ASJC Scopus subject areas

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