A novel DNA sequence compression scheme using both intra and inter sequences correlation

K. O. Cheng; Ngai Fong Law; W. C. Siu

doi:10.1109/APSIPA.2015.7415512

A novel DNA sequence compression scheme using both intra and inter sequences correlation

K. O. Cheng, Ngai Fong Law, W. C. Siu

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

Abstract

Classical DNA sequence compression algorithms consider only intra-sequence similarity, i.e., similar subsequences within the DNA sequence are found and encoded together. In this work, in addition to the intra-sequence similarity, we exploit the inter-sequence similarities in that similar subsequences are found within the DNA sequence as well as from other reference sequences. Hence, highly similar sequences from the same population or partially similar chromosome sequences of the same species can be compressed together to reduce the storage space. Experimental results show that the proposed scheme achieves good compressibility for both partially similar chromosome sequences and highly similar population sequences.

Original language	English
Title of host publication	2015 Asia-Pacific Signal and Information Processing Association Annual Summit and Conference, APSIPA ASC 2015
Publisher	IEEE
Pages	237-241
Number of pages	5
ISBN (Electronic)	9789881476807
DOIs	https://doi.org/10.1109/APSIPA.2015.7415512
Publication status	Published - 19 Feb 2016
Event	2015 Asia-Pacific Signal and Information Processing Association Annual Summit and Conference, APSIPA ASC 2015 - Hong Kong, Hong Kong Duration: 16 Dec 2015 → 19 Dec 2015

Conference

Conference	2015 Asia-Pacific Signal and Information Processing Association Annual Summit and Conference, APSIPA ASC 2015
Country	Hong Kong
City	Hong Kong
Period	16/12/15 → 19/12/15

ASJC Scopus subject areas

Artificial Intelligence
Modelling and Simulation
Signal Processing

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10.1109/APSIPA.2015.7415512

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abstract = "Classical DNA sequence compression algorithms consider only intra-sequence similarity, i.e., similar subsequences within the DNA sequence are found and encoded together. In this work, in addition to the intra-sequence similarity, we exploit the inter-sequence similarities in that similar subsequences are found within the DNA sequence as well as from other reference sequences. Hence, highly similar sequences from the same population or partially similar chromosome sequences of the same species can be compressed together to reduce the storage space. Experimental results show that the proposed scheme achieves good compressibility for both partially similar chromosome sequences and highly similar population sequences.",

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Cheng, KO, Law, NF & Siu, WC 2016, A novel DNA sequence compression scheme using both intra and inter sequences correlation. in 2015 Asia-Pacific Signal and Information Processing Association Annual Summit and Conference, APSIPA ASC 2015., 7415512, IEEE, pp. 237-241, 2015 Asia-Pacific Signal and Information Processing Association Annual Summit and Conference, APSIPA ASC 2015, Hong Kong, Hong Kong, 16/12/15. https://doi.org/10.1109/APSIPA.2015.7415512

A novel DNA sequence compression scheme using both intra and inter sequences correlation. / Cheng, K. O.; Law, Ngai Fong; Siu, W. C.

2015 Asia-Pacific Signal and Information Processing Association Annual Summit and Conference, APSIPA ASC 2015. IEEE, 2016. p. 237-241 7415512.

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

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A novel DNA sequence compression scheme using both intra and inter sequences correlation

Abstract

Conference

ASJC Scopus subject areas

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