DNA Lossless Differential Compression Algorithm based on Similarity of Genomic Sequence Database

Heba Afify; Muhammad Islam; Manal Abdel Wahed

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arXiv · 1109.0094

DNA Lossless Differential Compression Algorithm based on Similarity of Genomic Sequence Database

Heba Afify·Muhammad Islam·Manal Abdel Wahed

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Abstract

Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information theory are often perceived as being of interest for data communication and storage. In recent years, a substantial effort has been made for the application of textual data compression techniques to various computational biology tasks, ranging from storage and indexing of large datasets to comparison of genomic databases. This paper presents a differential compression algorithm that is based on production of difference sequences according to op-code table in order to optimize the compression of homologous sequences in dataset. Therefore, the stored data are composed of reference sequence, the set of differences, and differences locations, instead of storing each sequence individually. This algorithm does not require a priori knowledge about the statistics of the sequence set. The algorithm was applied to three different datasets of genomic sequences, it achieved up to 195-fold compression rate corresponding to 99.4% space saving.

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Heba Afify, Muhammad Islam, Manal Abdel Wahed. 2011-09-01. DNA Lossless Differential Compression Algorithm based on Similarity of Genomic Sequence Database. https://arxiv.org/abs/1109.0094

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