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miRDeep*：一个从 RNA 测序数据中识别 miRNA 的综合应用工具。

miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data.

机构信息

Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation (IHBI), Queensland University of Technology, Princess Alexandra Hospital, Level 1, Building 1, Ipswich Road, Brisbane, Queensland, QLD 4102, Australia.

出版信息

Nucleic Acids Res. 2013 Jan;41(2):727-37. doi: 10.1093/nar/gks1187. Epub 2012 Dec 4.

DOI:10.1093/nar/gks1187
PMID:23221645
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3553977/
Abstract

miRDeep and its varieties are widely used to quantify known and novel micro RNA (miRNA) from small RNA sequencing (RNAseq). This article describes miRDeep*, our integrated miRNA identification tool, which is modeled off miRDeep, but the precision of detecting novel miRNAs is improved by introducing new strategies to identify precursor miRNAs. miRDeep* has a user-friendly graphic interface and accepts raw data in FastQ and Sequence Alignment Map (SAM) or the binary equivalent (BAM) format. Known and novel miRNA expression levels, as measured by the number of reads, are displayed in an interface, which shows each RNAseq read relative to the pre-miRNA hairpin. The secondary pre-miRNA structure and read locations for each predicted miRNA are shown and kept in a separate figure file. Moreover, the target genes of known and novel miRNAs are predicted using the TargetScan algorithm, and the targets are ranked according to the confidence score. miRDeep* is an integrated standalone application where sequence alignment, pre-miRNA secondary structure calculation and graphical display are purely Java coded. This application tool can be executed using a normal personal computer with 1.5 GB of memory. Further, we show that miRDeep* outperformed existing miRNA prediction tools using our LNCaP and other small RNAseq datasets. miRDeep* is freely available online at http://www.australianprostatecentre.org/research/software/mirdeep-star.

摘要

miRDeep 及其变体被广泛用于从小 RNA 测序 (RNAseq) 中定量已知和新的 microRNA (miRNA)。本文描述了 miRDeep*，这是我们的集成 miRNA 识别工具，它是基于 miRDeep 建模的，但通过引入新的策略来识别前体 miRNA，提高了检测新 miRNA 的精度。miRDeep* 具有用户友好的图形界面，可接受 FastQ 和序列比对图 (SAM) 或二进制等效 (BAM) 格式的原始数据。通过读取次数测量的已知和新的 miRNA 表达水平显示在一个界面中，该界面显示每个 RNAseq 读取相对于前体 miRNA 发夹的相对位置。显示每个预测 miRNA 的二级前体 miRNA 结构和读取位置，并将其保存在单独的图形文件中。此外，使用 TargetScan 算法预测已知和新 miRNA 的靶基因，并根据置信分数对靶基因进行排序。miRDeep* 是一个集成的独立应用程序，其中序列比对、前体 miRNA 二级结构计算和图形显示都是纯 Java 编码的。该应用程序工具可以在具有 1.5GB 内存的普通个人计算机上执行。此外，我们还展示了 miRDeep* 使用我们的 LNCaP 和其他小 RNAseq 数据集在现有的 miRNA 预测工具中表现更好。miRDeep* 可在 http://www.australianprostatecentre.org/research/software/mirdeep-star 上免费在线获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ec1/3553977/f0b28abee665/gks1187f4p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ec1/3553977/344a4f5896b8/gks1187f1p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ec1/3553977/b95a4a578a92/gks1187f2p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ec1/3553977/40457e3e65ea/gks1187f3p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ec1/3553977/f0b28abee665/gks1187f4p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ec1/3553977/344a4f5896b8/gks1187f1p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ec1/3553977/b95a4a578a92/gks1187f2p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ec1/3553977/40457e3e65ea/gks1187f3p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ec1/3553977/f0b28abee665/gks1187f4p.jpg

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