序列空间中的统计几何学：一种定量比较序列分析方法。
Statistical geometry in sequence space: a method of quantitative comparative sequence analysis.
作者信息
Eigen M, Winkler-Oswatitsch R, Dress A
机构信息
Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Federal Republic of Germany.
出版信息
Proc Natl Acad Sci U S A. 1988 Aug;85(16):5913-7. doi: 10.1073/pnas.85.16.5913.
Abstract
A statistical method of comparative sequence analysis that combines horizontal and vertical correlations among aligned sequences is introduced. It is based on the analysis mainly of quartet combinations of sequences considered as geometric configurations in sequence space. Numerical invariants related to relative internal segment lengths are assigned to each such configuration and statistical averages of these invariants are established. They are used for internal calibration of the topology of divergence and for quantitative determination of the noise level. Comparison of computer simulations with experimental data reveals the high sensitivity of assignment of basic topologies even if much randomized. In addition, these procedures are checked by vertical analysis of the aligned sequences to allow the study of divergences with positionally varying substitution probabilities.
摘要
介绍了一种结合比对序列间水平和垂直相关性的比较序列分析统计方法。它主要基于对序列四重组合的分析，这些序列四重组合在序列空间中被视为几何构型。与相对内部片段长度相关的数值不变量被分配给每个这样的构型，并建立这些不变量的统计平均值。它们用于分歧拓扑的内部校准和噪声水平的定量测定。计算机模拟与实验数据的比较表明，即使存在大量随机化，基本拓扑的分配仍具有很高的灵敏度。此外，通过对比对序列的垂直分析来检验这些程序，以便研究具有位置变化替换概率的分歧。
相似文献
1
Statistical geometry in sequence space: a method of quantitative comparative sequence analysis.序列空间中的统计几何学：一种定量比较序列分析方法。
Proc Natl Acad Sci U S A. 1988 Aug;85(16):5913-7. doi: 10.1073/pnas.85.16.5913.
2
GEOSEQ: a Pascal program to calculate statistical geometry parameters of aligned nucleic acid sequences.GEOSEQ：一个用于计算比对核酸序列统计几何参数的Pascal程序。
Comput Appl Biosci. 1992 Aug;8(4):385-8. doi: 10.1093/bioinformatics/8.4.385.
3
Graphs in sequence spaces: a review of statistical geometry.序列空间中的图：统计几何综述
Biophys Chem. 1997 Jun 30;66(2-3):111-31. doi: 10.1016/s0301-4622(97)00064-1.
4
Assessment and statistical modeling of the relationship between remotely sensed aerosol optical depth and PM2.5 in the eastern United States.美国东部地区遥感气溶胶光学厚度与PM2.5之间关系的评估及统计建模
Res Rep Health Eff Inst. 2012 May(167):5-83; discussion 85-91.
5
Comparison study on k-word statistical measures for protein: from sequence to 'sequence space'.蛋白质的k字统计量比较研究：从序列到“序列空间”
BMC Bioinformatics. 2008 Sep 23;9:394. doi: 10.1186/1471-2105-9-394.
6
Detection of correlations in tRNA sequences with structural implications.检测具有结构意义的tRNA序列中的相关性。
Proc Int Conf Intell Syst Mol Biol. 1993;1:225-33.
7
Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site.当替换率随位点变化时，最大似然法、邻接法和最大简约法的相对效率。
Mol Biol Evol. 1994 Mar;11(2):261-77. doi: 10.1093/oxfordjournals.molbev.a040108.
8
A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.同源蛋白质的一种构象空间，其保留互信息并允许基于成对Z分数概率进行系统发育推断。
BMC Bioinformatics. 2005 Mar 10;6:49. doi: 10.1186/1471-2105-6-49.
9
Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants.利用系统发育一致性和马尔可夫不变量开发一种用于四重树推断的具有统计学效力的方法。
J Math Biol. 2017 Dec;75(6-7):1619-1654. doi: 10.1007/s00285-017-1129-2. Epub 2017 Apr 22.
10
Quartet-mapping, a generalization of the likelihood-mapping procedure.四重映射，似然映射程序的一种推广。
Mol Biol Evol. 2001 Jul;18(7):1204-19. doi: 10.1093/oxfordjournals.molbev.a003907.
引用本文的文献
1
Motifs in SARS-CoV-2 evolution.SARS-CoV-2 进化中的基序。
RNA. 2023 Dec 18;30(1):1-15. doi: 10.1261/rna.079557.122.
2
A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics.一种新的系统发育分析方法：应对分子系统发育中的模型误设和确认偏差
NAR Genom Bioinform. 2020 Jun 23;2(2):lqaa041. doi: 10.1093/nargab/lqaa041. eCollection 2020 Jun.
3
Neutral components show a hierarchical community structure in the genotype-phenotype map of RNA secondary structure.在RNA二级结构的基因型-表型图谱中，中性成分呈现出分层的群落结构。
J R Soc Interface. 2020 Oct;17(171):20200608. doi: 10.1098/rsif.2020.0608. Epub 2020 Oct 21.
4
Phylogenetic Network of Mitochondrial COI Gene Sequences Distinguishes 10 Taxa Within the Neotropical Albitarsis Group (Diptera: Culicidae), Confirming the Separate Species Status of Anopheles albitarsis H (Diptera: Culicidae) and Revealing a Novel Lineage, Anopheles albitarsis J.线粒体 COI 基因序列的系统发育网络区分了新热带疟蚊属中的 10 个种，证实了按蚊属白足亚种（双翅目：蚊科）的独立种地位，并揭示了一个新的谱系，即按蚊属白足亚种 J.
J Med Entomol. 2021 Mar 12;58(2):599-607. doi: 10.1093/jme/tjaa211.
5
Using small samples to estimate neutral component size and robustness in the genotype-phenotype map of RNA secondary structure.使用小样本估计 RNA 二级结构基因型-表型图谱中中性成分的大小和稳健性。
J R Soc Interface. 2020 May;17(166):20190784. doi: 10.1098/rsif.2019.0784. Epub 2020 May 20.
6
From pairs of most similar sequences to phylogenetic best matches.从最相似序列对到系统发育最佳匹配。
Algorithms Mol Biol. 2020 Apr 9;15:5. doi: 10.1186/s13015-020-00165-2. eCollection 2020.
7
Phylogenetics beyond biology.生物学之外的系统发育学。
Theory Biosci. 2018 Nov;137(2):133-143. doi: 10.1007/s12064-018-0264-7. Epub 2018 Jun 21.
8
Phenotypes can be robust and evolvable if mutations have non-local effects on sequence constraints.如果突变对序列约束具有非局部效应，那么表型可以是稳健和可进化的。
J R Soc Interface. 2018 Jan;15(138). doi: 10.1098/rsif.2017.0618.
9
The diversification of begomovirus populations is predominantly driven by mutational dynamics.菜豆金色花叶病毒属病毒群体的多样化主要由突变动态驱动。
Virus Evol. 2017 Mar 2;3(1):vex005. doi: 10.1093/ve/vex005. eCollection 2017 Jan.
10
Selecting informative subsets of sparse supermatrices increases the chance to find correct trees.选择稀疏超矩阵的信息子集可以增加找到正确树的机会。
BMC Bioinformatics. 2013 Dec 3;14:348. doi: 10.1186/1471-2105-14-348.
本文引用的文献
1
Optimization by simulated annealing.模拟退火优化。
Science. 1983 May 13;220(4598):671-80. doi: 10.1126/science.220.4598.671.
2
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.一种通过核苷酸序列比较研究来估计碱基替换进化速率的简单方法。
J Mol Evol. 1980 Dec;16(2):111-20. doi: 10.1007/BF01731581.
3
Accuracy of estimated phylogenetic trees from molecular data. I. Distantly related species.基于分子数据的系统发育树估计的准确性。I. 远缘物种
J Mol Evol. 1982;18(6):387-404. doi: 10.1007/BF01840887.
4
Transfer-RNA: the early adaptor.转运核糖核酸：早期的衔接分子。
Naturwissenschaften. 1981 May;68(5):217-28. doi: 10.1007/BF01047323.
5
6
Suggested model for prebiotic evolution: the use of chaos.益生元进化的建议模型：混沌的利用。
Proc Natl Acad Sci U S A. 1983 Jun;80(11):3386-90. doi: 10.1073/pnas.80.11.3386.
7
Natural selection and the concept of a protein space.自然选择与蛋白质空间的概念。
Nature. 1970 Feb 7;225(5232):563-4. doi: 10.1038/225563a0.
8
Construction of phylogenetic trees.系统发育树的构建。
Science. 1967 Jan 20;155(3760):279-84. doi: 10.1126/science.155.3760.279.
9
Selforganization of matter and the evolution of biological macromolecules.物质的自组织与生物大分子的进化
Naturwissenschaften. 1971 Oct;58(10):465-523. doi: 10.1007/BF00623322.
10
Pattern analysis of 5S rRNA.5S核糖体RNA的模式分析
Proc Natl Acad Sci U S A. 1985 Apr;82(8):2437-41. doi: 10.1073/pnas.82.8.2437.
Zotero 插件