English

A DNA Sequence Compression Algorithm Based on LUT and LZ77

Information Theory 2007-07-16 v6 math.IT
Authors: Sheng Bao , Shi Chen , Zhiqiang Jing , Ran Ren
View on arXiv ↗ PDF ↗

Abstract

This article introduces a new DNA sequence compression algorithm which is based on LUT and LZ77 algorithm. Combined a LUT-based pre-coding routine and LZ77 compression routine,this algorithm can approach a compression ratio of 1.9bits \slash base and even lower.The biggest advantage of this algorithm is fast execution, small memory occupation and easy implementation.

Cite

@article{arxiv.cs/0504100,
  title  = {A DNA Sequence Compression Algorithm Based on LUT and LZ77},
  author = {Sheng Bao and Shi Chen and Zhiqiang Jing and Ran Ren},
  journal= {arXiv preprint arXiv:cs/0504100},
  year   = {2007}
}

Comments

13 pages,3 tables,with source code of our algorithm

Related papers

View all related →
Information Theory · Computer Science
A Fixed-Length Coding Algorithm for DNA Sequence Compression
Jie Liu, Sheng Bao, Zhiqiang Jing, Shi Chen
2007-07-16
Computational Engineering, Finance, and Science · Computer Science
Engineering Relative Compression of Genomes
Szymon Grabowski, Sebastian Deorowicz
2011-03-14
Computational Engineering, Finance, and Science · Computer Science
An Efficient Biological Sequence Compression Technique Using LUT And Repeat In The Sequence
Subhankar Roy, Sunirmal Khatua, Sudipta Roy, Samir K. Bandyopadhyay
2012-11-13
Mathematical Software · Computer Science
Genbit Compress Tool(GBC): A Java-Based Tool to Compress DNA Sequences and Compute Compression Ratio(bits/base) of Genomes
P. Raja Rajeswari, Allam Apparo, V. K. Kumar
2010-07-15
Data Structures and Algorithms · Computer Science
DNA Lossless Differential Compression Algorithm based on Similarity of Genomic Sequence Database
Heba Afify, Muhammad Islam, Manal Abdel Wahed
2011-09-05
Information Theory · Computer Science
Reference Based Genome Compression
Bobbie Chern, Idoia Ochoa, Alexandros Manolakos, Albert No +2
2016-11-15
Quantitative Methods · Quantitative Biology
Genetic Sequence compression using Machine Learning and Arithmetic Encoding Decoding Techniques
Mehedi Hasan Sarkar, Adnan Ferdous Ashrafi
2023-03-10
Data Structures and Algorithms · Computer Science
Disk-based genome sequencing data compression
Szymon Grabowski, Sebastian Deorowicz, Łukasz Roguski
2014-09-19
Emerging Technologies · Computer Science
DNA-Based Storage: Trends and Methods
S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Eva Ruiz Garcia, Jian Ma +2
2015-07-08
Other Quantitative Biology · Quantitative Biology
Analysis of Compression Techniques for DNA Sequence Data
Shakeela Bibi, Javed Iqbal, Adnan Iftekhar, Mir Hassan
2020-06-04
Information Theory · Computer Science
Coding for Optimized Writing Rate in DNA Storage
Siddharth Jain, Farzad Farnoud, Moshe Schwartz, Jehoshua Bruck
2020-05-14
Data Structures and Algorithms · Computer Science
Compression of high throughput sequencing data with probabilistic de Bruijn graph
Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Guillaume Rizk
2014-12-19
Genomics · Quantitative Biology
DNA Sequence Classification with Compressors
Şükrü Ozan
2024-01-26
Image and Video Processing · Electrical Eng. & Systems
A biologically constrained encoding solution for long-term storage of images onto synthetic DNA
Melpomeni Dimopoulou, Marc Antonini, Pascal Barbry, Raja Appuswamy
2019-04-08
Quantitative Methods · Quantitative Biology
Reference Sequence Construction for Relative Compression of Genomes
Shanika Kuruppu, Simon Puglisi, Justin Zobel
2011-06-21
Information Theory · Computer Science
FastqZip: An Improved Reference-Based Genome Sequence Lossy Compression Framework
Yuanjian Liu, Huihao Luo, Zhijun Han, Yao Hu +5
2024-04-04
Computer Vision and Pattern Recognition · Computer Science
Fast low-level pattern matching algorithm
Janja Paliska Soldo, Ana Sovic Krzic, and Damir Sersic
2016-11-21
Data Structures and Algorithms · Computer Science
A Compressed Self-Index for Genomic Databases
Travis Gagie, Juha Kärkkäinen, Yakov Nekrich, Simon J. Puglisi
2011-11-08
Information Theory · Computer Science
Optimizing Sequencing Coverage Depth in DNA Storage: Insights From DNA Storage Data
Ruiying Cao, Xin Chen
2025-04-22
Data Structures and Algorithms · Computer Science
Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform
Anthony J. Cox, Markus J. Bauer, Tobias Jakobi, Giovanna Rosone
2015-03-20
Information Theory · Computer Science
Deep DNA Storage: Scalable and Robust DNA Storage via Coding Theory and Deep Learning
Daniella Bar-Lev, Itai Orr, Omer Sabary, Tuvi Etzion +1
2024-03-13
Genomics · Quantitative Biology
Lossy Compression of Quality Values via Rate Distortion Theory
Himanshu Asnani, Dinesh Bharadia, Mainak Chowdhury, Idoia Ochoa +2
2012-07-24
Emerging Technologies · Computer Science
DNA data storage, sequencing data-carrying DNA
Jasmine Quah, Omer Sella, Thomas Heinis
2022-05-12
Image and Video Processing · Electrical Eng. & Systems
MQ-Coder inspired arithmetic coder for synthetic DNA data storage
Xavier Pic, Melpomeni Dimopoulou, Eva Gil San Antonio, Marc Antonini
2023-09-15
Information Theory · Computer Science
Concatenated Code Design for Constrained DNA Data Storage with Asymmetric Errors
Yixin Wang, Li Deng, Md. Noor-A-Rahim, Erry Gunawan +3
2021-12-20