一种用于估计大量同源DNA序列数据集中位点间替换率变异的新方法。
A novel method for estimating substitution rate variation among sites in a large dataset of homologous DNA sequences.
作者信息
Pesole G, Saccone C
机构信息
Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, via Celoria 26, 20133 Milano, Italy.
出版信息
Genetics. 2001 Feb;157(2):859-65. doi: 10.1093/genetics/157.2.859.
Abstract
We present here a novel method to estimate the site-specific relative variability in large sets of homologous sequences. It is based on the simple idea that the more closely related are the compared sequences, the higher the probability of observing nucleotide changes at rapidly evolving sites. A simulation study has been carried out to support the reliability of the method, which has been applied also to analyzing the site variability of all available human sequences corresponding to the two hypervariable regions of the mitochondrial D-loop.
摘要
我们在此提出一种新方法，用于估计大量同源序列中位点特异性相对变异性。它基于一个简单的理念，即比较的序列关系越密切，在快速进化位点观察到核苷酸变化的概率就越高。已进行了一项模拟研究以支持该方法的可靠性，该方法也已应用于分析与线粒体D环两个高变区相对应的所有可用人类序列的位点变异性。
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本文引用的文献
1
Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees.人类和黑猩猩线粒体高变区I中各位点间的替换率差异。
Mol Biol Evol. 1999 Oct;16(10):1357-68. doi: 10.1093/oxfordjournals.molbev.a026046.
2
Inferring the historical patterns of biological evolution.推断生物进化的历史模式。
Nature. 1999 Oct 28;401(6756):877-84. doi: 10.1038/44766.
3
Aging-dependent large accumulation of point mutations in the human mtDNA control region for replication.人类线粒体DNA复制控制区中与衰老相关的点突变大量积累。
Science. 1999 Oct 22;286(5440):774-9. doi: 10.1126/science.286.5440.774.
4
Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA.人类线粒体DNA高变区I和II中的核苷酸替换模式及速率异质性
Genetics. 1999 Jul;152(3):1103-10. doi: 10.1093/genetics/152.3.1103.
5
Mitochondrial mutation rate revisited: hot spots and polymorphism.重新审视线粒体突变率：热点与多态性。
Nat Genet. 1998 Feb;18(2):109-10. doi: 10.1038/ng0298-109.
6
Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications.哺乳动物线粒体D环区域结构分析：新保守序列的鉴定及其功能和进化意义
Gene. 1997 Dec 31;205(1-2):125-40. doi: 10.1016/s0378-1119(97)00404-6.
7
Compilation of human mtDNA control region sequences.人类线粒体DNA控制区序列的汇编。
Nucleic Acids Res. 1998 Jan 1;26(1):126-9. doi: 10.1093/nar/26.1.126.
8
MITOMAP: a human mitochondrial genome database--1998 update.线粒体基因组数据库（MITOMAP）：1998年更新版
Nucleic Acids Res. 1998 Jan 1;26(1):112-5. doi: 10.1093/nar/26.1.112.
9
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Comput Appl Biosci. 1997 Oct;13(5):555-6. doi: 10.1093/bioinformatics/13.5.555.
10
A simple method for estimating the parameter of substitution rate variation among sites.一种估计位点间替换率变化参数的简单方法。
Mol Biol Evol. 1997 Nov;14(11):1106-13. doi: 10.1093/oxfordjournals.molbev.a025720.
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