Mapping the space of genomic signatures.
Mapping the space of genomic signatures.
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DOI：
10.1371/journal.pone.0119815
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Dattani NS
中科院分区：
文献类型：
--
作者：
Kari L;Hill KA;Sayem AS;Karamichalis R;Bryans N;Davis K;Dattani NS
我们提出了一种计算方法来测量和可视化任意数量的DNA序列之间的相互关系，例如，允许检查数百或数千个完整的线粒体基因组。对于DNA序列的每一对图形表示，计算出一个图像距离，并将距离可视化为分子距离图：图上的每个点代表一个DNA序列，任何两个点之间的空间接近程度反映了相应序列之间的结构相似程度。DNA序列的图形表示，混沌游戏表示(CGR)，是基因组和物种特有的，因此可以作为基因组签名。因此，分子距离图可以为物种鉴定、分类以及一定程度上的进化史提供信息。所使用的图像距离，结构相异指数(DSSIM)，隐含地比较了DNA序列中长度最大为k(这里k=9)的低聚物的出现。我们计算了500多万对完整线粒体基因组的DSSIM距离，并使用多维缩放(MDS)获得了分子距离图，该图直观地显示了不同分类水平上不同子集的序列相关性。这种通用方法不需要DNA序列比对，因此可以用来比较相同或不同长度的相似或非常不同的DNA序列，无论是基因组序列还是计算机生成的DNA序列。我们通过将其应用于几个分类亚集来说明这种方法的潜在用途：脊椎动物门、(超级)原生动物界、两栖纲-昆虫纲-哺乳动物纲、两栖纲和灵长目动物。这一对大量数据集的分析证实，完整mtDNA序列的寡聚体组成可以作为分类学信息的来源。这种方法还正确地找到了与现代人(尼安德特人、丹尼索瓦人和黑猩猩)在解剖学上最接近的mtDNA序列，并且在这个数据集中与之最不同的序列属于黄瓜。
We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to k (herein k = 9) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence alignment and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information. This method also correctly finds the mtDNA sequences most closely related to that of the anatomically modern human (the Neanderthal, the Denisovan, and the chimp), and that the sequence most different from it in this dataset belongs to a cucumber.
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DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
影响因子：
3.1
作者：
Hill, KA;Singh, SM
通讯作者：
Singh, SM
DOI：
10.2307/2992184
发表时间：
1990-09-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
LESSA, EP
通讯作者：
LESSA, EP
影响因子：
1.3
作者：
Beadell, JS;Fleischer, RC
通讯作者：
Fleischer, RC
影响因子：
3.2
作者：
Jameson, Natalie M.;Hou, Zhuo-Cheng;Wildman, Derek E.
通讯作者：
Wildman, Derek E.