miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining.
miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining.
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miRNA Digger：全基因组新颖 miRNA 挖掘的综合管道
DOI：
10.1038/srep18901
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发表时间：
2016-01-06
影响因子：
4.6
通讯作者：
Chen M
中科院分区：
文献类型：
--
作者：
Yu L;Shao C;Ye X;Meng Y;Zhou Y;Chen M
microRNA（mirnas）是基因表达的重要调节剂。加密数据在这方面，通过基于脱生物的敏感性和可靠性，在这方面开发了一种新型工具，用于系统地发现miRNA候选者。众所周知，在目标预测后发现了四个没有在Mirbase中注册的新型Mirna-mirna*对，并在基于数据的验证中发现了涉及Mirna的六个Mirna distection。 http://www.bioinfolab.cn/mirna_digger/index.html。
MicroRNAs (miRNAs) are important regulators of gene expression. The recent advances in high-throughput sequencing (HTS) technique have greatly facilitated large-scale detection of the miRNAs. However, thoroughly discovery of novel miRNAs from the available HTS data sets remains a major challenge. In this study, we observed that Dicer-mediated cleavage sites for the processing of the miRNA precursors could be mapped by using degradome sequencing data in both animals and plants. In this regard, a novel tool, miRNA Digger, was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. To test its sensitivity and reliability, miRNA Digger was applied to discover miRNAs from four organs ofArabidopsis. The results revealed that a majority of already known mature miRNAs along with their miRNA*s expressed in these four organs were successfully recovered. Notably, a total of 30 novel miRNA-miRNA* pairs that have not been registered in miRBase were discovered by miRNA Digger. After target prediction and degradome sequencing data-based validation, eleven miRNA–target interactions involving six of the novel miRNAs were identified. Taken together, miRNA Digger could be applied for sensitive detection of novel miRNAs and it could be freely downloaded from http://www.bioinfolab.cn/miRNA_Digger/index.html.