基于粗粒化二级结构点图的无比对基因组学方法筛选结构 RNA。
Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots.
机构信息
Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan.
Center for non-coding RNA in Technology and Health (RTH), University of Copenhagen, Groennegaardsvej 3, Frederiksberg, 1870, Denmark.
出版信息
BMC Genomics. 2017 Dec 2;18(1):935. doi: 10.1186/s12864-017-4309-y.
BACKGROUND
Structured non-coding RNAs play many different roles in the cells, but the annotation of these RNAs is lacking even within the human genome. The currently available computational tools are either too computationally heavy for use in full genomic screens or rely on pre-aligned sequences.
METHODS
Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level. This allows us to perform an all-against-all scan of all window pairs from two genomes without alignment.
RESULTS
Our computational experiments with simulated data and real chromosomes demonstrate that the presented method has good sensitivity.
CONCLUSIONS
DotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs.
背景
结构非编码 RNA 在细胞中发挥着多种不同的作用，但即使在人类基因组中，这些 RNA 的注释也很缺乏。目前可用的计算工具要么计算量过大，不适合用于全基因组筛选，要么依赖于预对齐的序列。
方法
在这里，我们提出了一种快速有效的方法 DotcodeR，通过在字符串级别比较其相应的粗粒度二级结构点图来检测基因组序列中结构相似的 RNA。这使得我们可以在不进行比对的情况下对两个基因组中的所有窗口对进行全对全扫描。
结果
我们用模拟数据和真实染色体进行的计算实验表明，所提出的方法具有很好的灵敏度。
结论
DotcodeR 可以作为结构 RNA 基因组比较扫描的预筛选器。
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