DNA-COMPACT: DNA COMpression Based on a Pattern-Aware Contextual Modeling Technique

Abstract

Genome data are becoming increasingly important for modern medicine. As the rate of increase in DNA sequencing outstrips the rate of increase in disk storage capacity, the storage and data transferring of large genome data are becoming important concerns for biomedical researchers. We propose a two-pass lossless genome compression algorithm, which highlights the synthesis of complementary contextual models, to improve the compression performance. The proposed framework could handle genome compression with and without reference sequences, and demonstrated performance advantages over best existing algorithms. The method for reference-free compression led to bit rates of 1.720 and 1.838 bits per base for bacteria and yeast, which were approximately 3.7% and 2.6% better than the state-of-the-art algorithms. Regarding performance with reference, we tested on the first Korean personal genome sequence data set, and our proposed method demonstrated a 189-fold compression rate, reducing the raw file size from 2986.8 MB to 15.8 MB at a comparable decompression cost with existing algorithms. DNAcompact is freely available at https://sourceforge.net/projects/dnacompact/for research purpose.

Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences

“…In 1993 the first specialized DNA compressor was proposed (Grumbach and Tahi, 1993). Since then, numerous DNA compressors were developed (e.g., Cao et al, 2007, Li et al, 2013, Benoit et al, 2015, Al-Okaily et al, 2017. In our experience only two compressors pass the practicality threshold: DELIMINATE (Mohammed et al, 2012) and MFCompress (Pinho and Pratas, 2014).…”

A Survey on Data Compression Methods for Biological Sequences

“…The DNA-COMPACT (DNA COMpression based on a Pattern-Aware Contextual modeling Technique) algorithm [45] exploits complementary contextual models and consists of two phases. In the first phase, the exact repeats and palindromes are searched and then represented by a compact quadruplet.…”

“…The DNA-COMPACT method [45], which can be used for both reference-free and reference-based genome compression, includes two phases. In the first phase, an adaptive mechanism, rLZ, is presented which firstly, considers a sliding window for the subsequences of the reference sequence; and secondly, searches for the longest exact repeats in the current fragment of the target sequence, in a bi-directional manner.…”

A New Lossless DNA Compression Algorithm Based on A Single-Block Encoding Scheme

“…The DNA-COMPACT (DNA COMpression) algorithm [42] based on a pattern-aware contextual modeling technique comprises of two phases. Firstly, it searched for exact repeats and palindromes by exploiting complementary contextual models and represent them by a compact quadruplet.…”