DNA-Residual: A DNA Compression Algorithm Using Forward Linear Prediction

Lina Karam (Inventor)

Research output: Patent

1 Citation (Scopus)

Abstract

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)
StatePublished - May 8 2006

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abstract = "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.",
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