Classification of Long Noncoding RNAs by k-mer Content.
Classification of Long Noncoding RNAs by k-mer Content.
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DOI：
10.1007/978-1-0716-1158-6_4
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发表时间：
2021
期刊：
影响因子：
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通讯作者：
Calabrese JM
中科院分区：
文献类型：
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作者：
Kirk JM;Sprague D;Calabrese JM
基于K-mer的比较已经成为BLAST类比对算法的有力补充，特别是当比较的序列缺乏直接的进化关系时。在这一章中，我们描述的方法来比较长的非编码RNA（lncRNA）组之间的k-聚体含量，以确定社区的lncRNA与相关的k-聚体含量，以确定富集的蛋白质结合基序lncRNA中，并扫描相关的lncRNA中的k-聚体内容的域。我们的分步说明由存放在Github中的Python代码补充。虽然本章的重点是lncRNA，但我们描述的方法可以应用于任何一组核酸序列。
K-mer based comparisons have emerged as powerful complements to BLAST-like alignment algorithms, particularly when the sequences being compared lack direct evolutionary relationships. In this chapter, we describe methods to compare k-mer content between groups of long noncoding RNAs (lncRNAs), to identify communities of lncRNAs with related k-mer contents, to identify the enrichment of protein-binding motifs in lncRNAs, and to scan for domains of related k-mer contents in lncRNAs. Our step-by-step instructions are complemented by Python code deposited in Github. Though our chapter focuses on lncRNAs, the methods we describe could be applied to any set of nucleic acid sequences.