NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes.
NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes.
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NATpipe：用于从头组装的转录组中系统地发现天然反义转录本 (NAT) 和相分布 nat-siRNA 的综合管道
DOI：
10.1038/srep21666
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发表时间：
2016-02-09
影响因子：
4.6
通讯作者：
Wang H
中科院分区：
文献类型：
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作者：
Yu D;Meng Y;Zuo Z;Xue J;Wang H
nat - sirna（小干扰RNA， small interfering RNA，源于天然反义转录物）是一类存在于动植物体内的功能性小RNA （sRNA）。这些sirna在NAT（天然反义转录物）对的退火区域内高度富集。迄今为止，对各种生物体中NATs的系统鉴定已经进行了大量的研究工作。然而，开发一个免费的、易于使用的NAT预测程序是研究人员强烈要求的。在这里，我们提出了一个名为NATpipe的整合管道，用于系统地从从头组装的转录组中发现nat。通过利用sRNA测序数据，该管道还允许用户在NAT对的完美退火区域内搜索相位分布的NAT - sirna。此外，基于降解组测序数据可以鉴定出更可靠的na - sirna位点。以非模式植物铁皮石斛为例，说明了NATpipe的实用性。最后，我们希望NATpipe能成为NAT预测、NAT - sirna发现和相关功能研究的有用工具。NATpipe可在www.bioinfolab.cn/NATpipe/NATpipe.zip上获得。
Nat-siRNAs (small interfering RNAs originated from natural antisense transcripts) are a class of functional small RNA (sRNA) species discovered in both plants and animals. These siRNAs are highly enriched within the annealed regions of the NAT (natural antisense transcript) pairs. To date, great research efforts have been taken for systematical identification of the NATs in various organisms. However, developing a freely available and easy-to-use program for NAT prediction is strongly demanded by researchers. Here, we proposed an integrative pipeline named NATpipe for systematical discovery of NATs from de novo assembled transcriptomes. By utilizing sRNA sequencing data, the pipeline also allowed users to search for phase-distributed nat-siRNAs within the perfectly annealed regions of the NAT pairs. Additionally, more reliable nat-siRNA loci could be identified based on degradome sequencing data. A case study on the non-model plant Dendrobium officinale was performed to illustrate the utility of NATpipe. Finally, we hope that NATpipe would be a useful tool for NAT prediction, nat-siRNA discovery, and related functional studies. NATpipe is available at www.bioinfolab.cn/NATpipe/NATpipe.zip.