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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >CLASSIFICATION AND IDENTIFICATION OF FUNGAL SEQUENCES USING CHARACTERISTIC RESTRICTION ENDONUCLEASE CUT ORDER
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CLASSIFICATION AND IDENTIFICATION OF FUNGAL SEQUENCES USING CHARACTERISTIC RESTRICTION ENDONUCLEASE CUT ORDER

机译：使用特征性限制性内切酶切割顺序对真菌序列进行分类和鉴定

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Restriction Fragment Length Polymorphism (RFLP) is a powerful molecular tool that isnextensively used in the molecular fingerprinting and epidemiological studies of microorganisms.nIn a wet-lab setting, the DNA is cut with one or more restriction enzymes andnsubjected to gel electrophoresis to obtain signature fragment patterns, which is utilizednin the classification and identification of organisms. This wet-lab approach may not benpractical when the experimental data set includes a large number of genetic sequencesnand a wide pool of restriction enzymes to choose from. In this study, we introduce annovel concept of Enzyme Cut Order — a biological property-based characteristic ofnDNA sequences which can be defined and analyzed computationally without any alignmentnalgorithm. In this alignment-free approach, a similarity matrix is developed basednon the pairwise Longest Common Subsequences (LCS) of the Enzyme Cut Orders. Thenchoice of an ideal set of restriction enzymes used for analysis is augmented by usingngenetic algorithms. The results obtained from this approach using internal transcribednspacer regions of rDNA from fungi as the target sequence show that the phylogeneticallyrelatednorganisms form a single cluster and successful grouping of phylogenetically closenor distant organisms is dependent on the choice of restriction enzymes used in the analysis.nAdditionally, comparison of trees obtained with this alignment-free and the legacynmethod revealed highly similar tree topologies. This novel alignment-free method, whichnutilizes the Enzyme Cut Order and restriction enzyme profile, is a reliable alternativento local or global alignment-based classification and identification of organisms
机译：限制性片段长度多态性（RFLP）是一种功能强大的分子工具，未广泛用于微生物的分子指纹和流行病学研究中。n在湿实验室中，DNA被一种或多种限制性酶切开，然后进行凝胶电泳以获得特征性片段模式，用于生物的分类和识别。当实验数据集包含大量遗传序列和大量限制酶可供选择时，这种湿实验室方法可能并不可行。在这项研究中，我们介绍了酶切单的新概念-一种基于生物学特性的nDNA序列特征，可以在没有任何比对算法的情况下进行定义和计算。在这种无比对方法中，基于酶切顺序的成对最长公共子序列（LCS），开发了相似性矩阵。然后使用遗传算法增加用于分析的一组理想的限制酶的选择。使用真菌中rDNA的内部转录间隔区作为靶序列，从该方法获得的结果表明，系统发育相关的生物形成单个簇，系统发育上最近或最远的生物的成功分组取决于分析中使用的限制性内切酶的选择。通过这种无路线和遗留方法获得的树木中，有许多树木的拓扑结构非常相似。这种新颖的无比对方法利用了酶切顺序和限制酶图谱，是基于局部或全局比对的生物分类和鉴定的可靠替代方法

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