DNA-residual: A DNA compression algorithm using forward linear prediction

Rony Ferzli, Lina J. Karam

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

This paper presents an efficient lossless DNA compression algorithm, DNA-Residual, that significantly decreases the average bit-rate required to losslessly code correlated DNA sequences. The algorithm can be divided into two parts: modeling and coding. The modeling part consists of mapping the DNA bases into a binary representation and, then, a forward linear prediction filter is used to predict the current input from the previous ones. The prediction error is then transformed into a binary error sequence that is coded using an adaptive binary arithmetic coder. Compared to state-of-the-art compressors using benchmark DNA sequences, the proposed algorithm reveals a significantly higher compression ratio whenever correlation between bases is high.

Original languageEnglish (US)
Title of host publication2006 IEEE International Conference on Acoustics, Speech, and Signal Processing - Proceedings
PagesII1100-II1103
StatePublished - Dec 1 2006
Event2006 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP 2006 - Toulouse, France
Duration: May 14 2006May 19 2006

Publication series

NameICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
Volume2
ISSN (Print)1520-6149

Other

Other2006 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP 2006
CountryFrance
CityToulouse
Period5/14/065/19/06

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ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Electrical and Electronic Engineering

Cite this

Ferzli, R., & Karam, L. J. (2006). DNA-residual: A DNA compression algorithm using forward linear prediction. In 2006 IEEE International Conference on Acoustics, Speech, and Signal Processing - Proceedings (pp. II1100-II1103). [1660539] (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings; Vol. 2).