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 Citation (Scopus)

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 publicationICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
Volume2
StatePublished - 2006
Event2006 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP 2006 - Toulouse, France
Duration: May 14 2006May 19 2006

Other

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

Fingerprint

linear prediction
DNA
deoxyribonucleic acid
DNA sequences
Compressors
compression ratio
compressors
coders
coding
filters
predictions

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Signal Processing
  • Acoustics and Ultrasonics

Cite this

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

DNA-residual : A DNA compression algorithm using forward linear prediction. / Ferzli, Rony; Karam, Lina J.

ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings. Vol. 2 2006. 1660539.

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

Ferzli, R & Karam, LJ 2006, DNA-residual: A DNA compression algorithm using forward linear prediction. in ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings. vol. 2, 1660539, 2006 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP 2006, Toulouse, France, 5/14/06.
Ferzli R, Karam LJ. DNA-residual: A DNA compression algorithm using forward linear prediction. In ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings. Vol. 2. 2006. 1660539
Ferzli, Rony ; Karam, Lina J. / DNA-residual : A DNA compression algorithm using forward linear prediction. ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings. Vol. 2 2006.
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