A Novel Quasi-Alignment-Based Method for Discovering Conserved Regions in Genetic Sequences

机译：一种基于准取向的遗传序列中的保守区域的新型对准方法

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摘要

This paper presents an alignment-free technique to efficiently discover similar regions in large sets of biological sequences using position sensitive p-mer frequency clustering. A set of sequences is broken down into segment and then a frequency distribution over all oligomers of size p (referred to as p-mers) is obtained to summarize each segment. These summaries are clustered while the order of segments in the set of sequences is preserved in a Markov-type model. Sequence segments within each cluster have very similar DNA/RNA patterns and form a so called quasi-alignment. This fact can be used for a variety of tasks such as species characterization and identification, phylogenetic analysis, functional analysis of sequences and, as in this paper, for discovering conserved regions. Our method is computationally more efficient than multiple sequences alignment since it can apply modern data stream clustering algorithms which run in time linear in the number of segments and thus can help discover highly similar regions across a large number of sequences efficiently. In this paper, we apply the approach to efficiently discover and visualize conserved regions in 16S rRNA.

机译：本文呈现了一种可对准的技术，可以使用位置敏感P-MER频率聚类有效地发现大型生物序列中的类似区域。将一组序列分解为片段，然后获得频率分布在尺寸P的所有低聚物（称为P-MERS）上总结每个段。这些摘要是群集的，而在Markov型模型中保留了该组序列集中的段的顺序。每个簇内的序列段具有非常相似的DNA / RNA图案，形成所谓的准取向。这一事实可用于各种任务，例如物种表征和鉴定，系统发育分析，序列功能分析，如本文用于发现保守区。我们的方法是多于多个序列对准的更有效，因为它可以应用现代数据流聚类算法，该算法在段的数量中运行时间线性，因此可以有助于有效地在大量序列上发现高度相似的区域。在本文中，我们应用了16S rRNA中有效地发现和可视化保守区域的方法。

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《International Conference on Bioinformatics and Biomedicine Workshops》|2012年||共8页
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Anurag Nagar; Michael Hahsler;
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中图分类 R318-532;
关键词
DNA/RNA sequences; quasi-alignment; multiple sequence alignment; conserved sequences;

机译：DNA / RNA序列;准对准;多序列对齐;保守序列;

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1. Discovery of conserved regions in DNA sequences by Artificial Bee Colony (ABC) algorithm based methods [J] . Karaboga Dervis, Aslan Selcuk Natural Computing . 2019,第2期

机译：通过基于人工蜂群（ABC）算法的方法发现DNA序列中的保守区
2. Discovery of conserved regions in DNA sequences by Artificial Bee Colony (ABC) algorithm based methods [J] . Karaboga Dervis, Aslan Selcuk Natural Computing . 2019,第2期

机译：基于人工蜂菌（ABC）算法的DNA序列中保守区域发现
3. Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. [J] . Stojanovic N, Florea L, Riemer C, Nucleic Acids Research . 1999,第19期

机译：在基因调控区的多重比对中寻找保守序列的五种方法的比较。
4. A novel quasi-alignment-based method for discovering conserved regions in genetic sequences [C] . Nagar Anurag, Hahsler Michael 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops. . 2012

机译：一种新的基于准比对的遗传序列保守区发现方法
5. Using phylogenetically conserved stress responses to discover natural products with anticancer activity. [D] . Turbyville, Thomas Jefferson. 2005

机译：使用系统发育上保守的应激反应来发现具有抗癌活性的天然产物。
6. Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. [O] . N Stojanovic, L Florea, C Riemer, 1999

机译：在基因调控区的多重比对中寻找保守序列的五种方法的比较。
7. Figure 7: The phylogenetic tree constructed from conserved regions of SGS3 protein sequences from 27 selected streptophytes by the Neighbor-Joining method with 1000 bootstrap replications. [O] . -1

机译：图7：由邻近27种选择的斜纹素的SGS3蛋白序列的保守区域构成的系统发育树由具有1000个引导复制的邻近的串联方法。

A Novel Quasi-Alignment-Based Method for Discovering Conserved Regions in Genetic Sequences

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