ED算法和SNP-index算法计算SNP位点的比较分析——以拟南芥为例

计算机工程与科学 ›› 2022, Vol. 44 ›› Issue (04): 707-712.

ED算法和SNP-index算法计算SNP位点的比较分析——以拟南芥为例

甘秋云

（福州理工学院应用科学与工程学院，福建福州 350014）

收稿日期:2020-05-15 修回日期:2020-12-10 接受日期:2022-04-25 出版日期:2022-04-25 发布日期:2022-04-20
基金资助:
福州理工学院校级科研基金（FTKY21053）

Comparison and analysis of ED algorithm and SNP-index algorithm in calculating SNP sites——Take arabidopsis thaliana for example

GAN Qiu-yun

(School of Applied Science and Engineering,Fuzhou Institute of Technology,Fuzhou 350014,China)

Received:2020-05-15 Revised:2020-12-10 Accepted:2022-04-25 Online:2022-04-25 Published:2022-04-20

摘要/Abstract

摘要： SNP（单核苷酸多态性）是发生在DNA序列上单个核苷酸碱基之间的变异,是生物可遗传变异中最常见的一种变异。ED算法和SNP-index算法是计算SNP位点的2种常用算法。由高通量测序获得拟南芥F2代全基因组测序数据，基于Linux平台对测序数据进行过滤、筛选和比对，通过算法实现结果，比较不同算法检测得到的SNP位点数量和SNP基因型比例。实验结果表明，通过ED算法得到的SNP位点数量更多，分布更广，相对分布密度大于SNP-index算法的，但是2种算法得到的SNP位点数量和SNP基因型比例相近。

关键词: 单核苷酸多态性（SNP）, 生物信息, ED算法, SNP-index算法

Abstract: SNP (Single Nucleotide Polymorphism) is the most common variation in biological heritable variation, which occurs between single nucleoside acid-base groups in DNA sequence. ED algorithm and SNP-index algorithm are two commonly used algorithms to calculate SNP sites. The whole genome sequencing data of F2 generation of arabidopsis thaliana are obtained by high-throughput sequencing. The sequencing data are filtered, screened and compared based on Linux platform. The number of SNP sites and the proportion of SNP genotypes detected under different algorithms are compared. The experimental results show that the number of SNP sites obtained by ED algorithm is more and more widely distributed than SNP index algorithm, and the relative distribution density is larger than that of SNP index algorithm, but the number of SNP sites and the proportion of SNP genotypes obtained by the two algorithms are similar.

Key words: single nucleotide polymorphism(SNP), biological information, ED algorithm, SNP-index algorithm

甘秋云. ED算法和SNP-index算法计算SNP位点的比较分析——以拟南芥为例[J]. 计算机工程与科学, 2022, 44(04): 707-712.

GAN Qiu-yun. Comparison and analysis of ED algorithm and SNP-index algorithm in calculating SNP sites——Take arabidopsis thaliana for example[J]. Computer Engineering & Science, 2022, 44(04): 707-712.

参考文献［9］

［1］	Ma Lei,Jia Qi-nan,Zhang Jun,et al.A novel computer based method for the selection of genetic loci with single nucleotide polymorphism［J］.Basic & Clinical Medicine,2014,34(2):229-234.(in Chinese)
［2］	Li R,Li Y,Fang X,et al.SNP detection for massively parallel whole-genome resequencing［J］.Genome Research,2009,19(6):1124-1132.
［3］	Taylor R C.An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics［J］.BMC Bioinformatics,2010,11(Suppl 12):495-499.
［4］	Li H.A statistical framework for SNP calling,mutation discovery,association mapping and population genetical parameter estimation from sequencing data［J］.Bioinformatics,2011,27(21):2987-2993.
［5］	Petr D,Shane A M.BCFtools/csq:Haplotype-aware variant consequences［J］.Bioinformatics,2017,33(13):2037-2039.
［6］	Hill J T,Demarest B L,Bisgrove B W,et al.MMAPPR:Mutation mapping analysis pipeline for pooled RNA-Seq［J］.Genome Research,2013,23(4):687-697.
［7］	Abe A,Kosugi S,Yoshida K,et al.Genome sequencing reveals agronomically important loci in rice using MutMap［J］.Nature Biotechnology,2012,30(2):174-178.
［8］	Jia Yu-yan,Chen Hong.Molecular genetic marker of single nucleotide polymorphism and its application［J］.Journal of Yellow Cattle Science,2003,29(1):42-45.(in Chinese)
［9］	Ge Jin-mei,Zhang Zhong-ying,Peng Xuan-xian,et al.Current status of single nucleotide polymorphism and its application in research of matrix metalloproteinases［J］. World Chinese Journal of Digestology,2005,13(17):2128-2137.(in Chinese)
	附中文参考文献：
［1］	马磊,贾奇男,张俊,等.一种基于计算机的单核苷酸多态性位点检测方法［J］.基础医学与临床,2014,34(2):229-234.
［8］	贾玉艳,陈宏.SNP分子标记的研究及应用［J］.黄牛杂志,2003，29(1):42-45.
［9］	葛金梅,张忠英,彭宣宪,等.SNP的研究现状及在MMPs研究中的应用［J］.世界华人消化杂志,2005,13(17):2128-2137.

[1]	潘玮华，陈波，徐云. 一种基于聚类的大规模单体分型算法[J]. J4, 2013, 35(11): 27-33.
[2]	菅晓东1,李扬1,冯景华1,孟祥飞1,朱小谦1，2. “天河一号”在生命科学研究中的应用[J]. J4, 2012, 34(8): 171-175.
[3]	金圣华,刘金岭. 基于核苷酸序列的探针水平数据分析[J]. J4, 2012, 34(11): 186-189.
[4]	夏〓飞，窦〓勇，雷国庆. 基于FPGA的非编码RNA基因检测算法加速器研究[J]. J4, 2011, 33(12): 153-158.
[5]	石金龙,骆志刚. 非负矩阵分解算法及其在生物信息学中的应用研究[J]. J4, 2010, 32(8): 117-123.
[6]	李锦钟诚卿海军. 基于分群策略的机群系统上Motif发现并行算法[J]. J4, 2008, 30(11): 126-128.
[7]	陈坚何洁月. 基于本体的生物信息集成技术发展现状[J]. J4, 2006, 28(12): 118-120.
[8]	王勇献王正华张振慧. 蛋白质结构预测算法的评估[J]. J4, 2005, 27(8): 62-64.
[9]	方小永骆志刚. DNA序列拼接的分布式并行处理[J]. J4, 2005, 27(2): 71-73.
[10]	陈传波雷昊. 生物信息工具软件的Web集成方案研究[J]. J4, 2004, 26(8): 66-69.
[11]	欧阳星明谢欣荣张少伟姚小龙. 分子三维结构可视化软件建模的研究与实现[J]. J4, 2004, 26(5): 25-28.