Intelligent DNA Sequence Data Compression Using Memetic Algorithm

ZHOU Jia-rui; JI Zhen; ZHU Ze-xuan; CHEN Si-ping

doi:10.3969/j.issn.0372-2112.2013.03.016

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Intelligent DNA Sequence Data Compression Using Memetic Algorithm

更新时间：2025-07-16

- Intelligent DNA Sequence Data Compression Using Memetic Algorithm
- Acta Electronica Sinica Vol. 41, Issue 3, Pages: 513-518(2013)
- 作者机构：
  
  1. 浙江大学生物医学工程与仪器科学学院,浙江,杭州,310027
  2. 深圳大学计算机与软件学院,广东,深圳,518060
  3. 深圳市嵌入式系统设计重点实验室,广东,深圳,518060
- 作者简介：
- 基金信息：
- DOI：10.3969/j.issn.0372-2112.2013.03.016
  CLC： TP391
- Published：2013
- 稿件说明：
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ZHOU Jia-rui, JI Zhen, ZHU Ze-xuan, et al. Intelligent DNA Sequence Data Compression Using Memetic Algorithm[J]. Acta Electronica Sinica, 2013, 41(3): 513-518.
DOI：

ZHOU Jia-rui, JI Zhen, ZHU Ze-xuan, et al. Intelligent DNA Sequence Data Compression Using Memetic Algorithm[J]. Acta Electronica Sinica, 2013, 41(3): 513-518. DOI： 10.3969/j.issn.0372-2112.2013.03.016.

摘要

提出近似重复矢量(Approximate Repeat Vector

ARV)模型用于DNA序列冗余片段的描述.通过将数据生物信息学特征引入压缩预处理

并使用ARV矢量构造编码码本

提出了非对称DNA序列压缩算法BioLZMA-2.算法引入基于粒子群优化的Memetic改进方法CLIPSO-MA用于压缩码本的智能优化设计

有效提升了编码性能.在标准测试序列上的实验结果表明

BioLZMA-2可获得比现有DNA序列数据压缩方法更高的压缩率.

Abstract

A data model namely the approximate repeat vector (ARV) is introduced to describe the similar fragments in DNA sequences.By employing bioinformatics features in data preprocessing

and using ARVs in compression codebook's construction

we propose an asymmetric DNA sequence compression algorithm of biological Lempel-Ziv-Markov chain algorithm 2(BioLZMA-2).The particle swarm optimization (PSO) based memetic algorithm improvement namely the comprehensive learning intelligent particle swarm optimization memetic algorithm (CLIPSO-MA) is employed in the compression codebook's design.Experimental results on benchmark sequences demonstrate better performance of BioLZMA-2 than the original DNA sequence compression algorithms.

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