Construction of random perfect phylogeny matrix.

Q2 Biochemistry, Genetics and Molecular Biology

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2010-01-01 Epub Date: 2010-11-16 DOI:10.2147/AABC.S13397

Mehdi Sadeghi, Hamid Pezeshk, Changiz Eslahchi, Sara Ahmadian, Sepideh Mah Abadi

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引用次数: 0

Abstract

Purpose: Interest in developing methods appropriate for mapping increasing amounts of genome-wide molecular data are increasing rapidly. There is also an increasing need for methods that are able to efficiently simulate such data.

Patients and methods: In this article, we provide a graph-theory approach to find the necessary and sufficient conditions for the existence of a phylogeny matrix with k nonidentical haplotypes, n single nucleotide polymorphisms (SNPs), and a population size of m for which the minimum allele frequency of each SNP is between two specific numbers a and b.

Results: We introduce an O(max(n(2), nm)) algorithm for the random construction of such a phylogeny matrix. The running time of any algorithm for solving this problem would be Ω (nm).

Conclusion: We have developed software, RAPPER, based on this algorithm, which is available at http://bioinf.cs.ipm.ir/softwares/RAPPER.

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随机完美系统发育矩阵的构建。

目的:对开发适合于绘制越来越多的全基因组分子数据的方法的兴趣正在迅速增加。对能够有效地模拟这些数据的方法的需求也在增加。在本文中，我们提供了一种图论方法来寻找一个系统发生矩阵存在的充分必要条件，该系统发生矩阵包含k个非相同单倍型，n个单核苷酸多态性(SNP)，以及m个种群大小，其中每个SNP的最小等位基因频率介于两个特定数字a和b之间。结果:我们引入了一个O(max(n(2)， nm))算法来随机构建这样的系统发生矩阵。任何解决这个问题的算法的运行时间都是Ω (nm)。结论:我们基于该算法开发了软件RAPPER，该软件可在http://bioinf.cs.ipm.ir/softwares/RAPPER上获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Advances and Applications in Bioinformatics and Chemistry Biochemistry, Genetics and Molecular Biology-Biochemistry, Genetics and Molecular Biology (miscellaneous)

CiteScore

6.50

自引率

0.00%

发文量

审稿时长

16 weeks