Toward a Better Compression for DNA Sequences Using Huffman Encoding

Al-okaily, Anas; Almarri, Badar; Yami, Sultan Al; Huang, Chun-Hsi

doi:10.1089/cmb.2016.0151

Cited by 23 publications

(19 citation statements)

References 12 publications

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“…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).…”

Section: Introductionmentioning

confidence: 88%

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

Kryukov

Ueda

Nakagawa

et al. 2018

Preprint

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DNA sequence databases use compression such as gzip to reduce the required storage space and network transmission time. We describe Nucleotide Archival Format (NAF)a new file format for lossless reference-free compression of FASTA and FASTQ-formatted nucleotide sequences. NAF compression ratio is comparable to the best DNA compressors, while providing dramatically faster decompression. We compared our format with DNA compressors: DELIMINATE and MFCompress, and with general purpose compressors: gzip, bzip2, xz, brotli, and zstd.Availability: NAF compressor and decompressor, as well as format specification are available at https://github.com/KirillKryukov/naf. Format specification is in public domain. Compressor and decompressor are open source under the zlib/libpng license, free for nearly any use.

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Section: Introductionmentioning

confidence: 88%

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

Kryukov

Ueda

Nakagawa

et al. 2018

Preprint

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“…UHT [34] DNA compression based on using Huffman coding. Unbalanced Huffman encoding/Tree, forcing the Huffman tree to be unbalanced to be better than the standard Huffman.…”

Section: Solution Contentsmentioning

confidence: 99%

“…UHTL [34] DNA compression based on using Huffman coding. Developed version of UHT that prioritizes encoding the k-mers that contain the least frequent base.…”

Section: Solution Contentsmentioning

confidence: 99%

BAQALC: Blockchain Applied Lossless Efficient Transmission of DNA Sequencing Data for Next Generation Medical Informatics

Lee¹,

Cho

Ikeno

et al. 2018

Applied Sciences

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Due to the development of high-throughput DNA sequencing technology, genome-sequencing costs have been significantly reduced, which has led to a number of revolutionary advances in the genetics industry. However, the problem is that compared to the decrease in time and cost needed for DNA sequencing, the management of such large volumes of data is still an issue. Therefore, this research proposes Blockchain Applied FASTQ and FASTA Lossless Compression (BAQALC), a lossless compression algorithm that allows for the efficient transmission and storage of the immense amounts of DNA sequence data that are being generated by Next Generation Sequencing (NGS). Also, security and reliability issues exist in public sequence databases. For methods, compression ratio comparisons were determined for genetic biomarkers corresponding to the five diseases with the highest mortality rates according to the World Health Organization. The results showed an average compression ratio of approximately 12 for all the genetic datasets used. BAQALC performed especially well for lung cancer genetic markers, with a compression ratio of 17.02. BAQALC performed not only comparatively higher than widely used compression algorithms, but also higher than algorithms described in previously published research. The proposed solution is envisioned to contribute to providing an efficient and secure transmission and storage platform for next-generation medical informatics based on smart devices for both researchers and healthcare users.

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“…It is required to reduce the storage size and the processing costs, as well as aid in fast searching retrieval information, and increase the transmission speed over the internet with limited bandwidth [13,22]. In general, compression can be either lossless or lossy; in lossless compression, no information is lost and the original data can be recovered exactly, while in lossy compression, only an approximation of the original data can be recovered [23][24][25][26]. Many researchers believe that lossless compression schemes are particularly needed for biological and medical data, which cannot afford to lose any part of their data [3].…”

mentioning

confidence: 99%

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

2020

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With the emergent evolution in DNA sequencing technology, a massive amount of genomic data is produced every day, mainly DNA sequences, craving for more storage and bandwidth. Unfortunately, managing, analyzing and specifically storing these large amounts of data become a major scientific challenge for bioinformatics. Therefore, to overcome these challenges, compression has become necessary. In this paper, we describe a new reference-free DNA compressor abbreviated as DNAC-SBE. DNAC-SBE is a lossless hybrid compressor that consists of three phases. First, starting from the largest base (Bi), the positions of each Bi are replaced with ones and the positions of other bases that have smaller frequencies than Bi are replaced with zeros. Second, to encode the generated streams, we propose a new single-block encoding scheme (SEB) based on the exploitation of the position of neighboring bits within the block using two different techniques. Finally, the proposed algorithm dynamically assigns the shorter length code to each block. Results show that DNAC-SBE outperforms state-of-the-art compressors and proves its efficiency in terms of special conditions imposed on compressed data, storage space and data transfer rate regardless of the file format or the size of the data.

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Toward a Better Compression for DNA Sequences Using Huffman Encoding

Cited by 23 publications

References 12 publications

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

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

BAQALC: Blockchain Applied Lossless Efficient Transmission of DNA Sequencing Data for Next Generation Medical Informatics

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

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