MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans.
MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans.
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MiRFinder：用于全基因组快速 microRNA 前体扫描的改进方法和软件实现
DOI：
10.1186/1471-2105-8-341
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发表时间：
2007-09-17
影响因子：
3
通讯作者：
Zhao, Shu-Hong
中科院分区：
文献类型：
--
作者：
Huang, Ting-Hua;Fan, Bin;Rothschild, Max F;Hu, Zhi-Liang;Li, Kui;Zhao, Shu-Hong
研究背景MicroRNAs（miRNAs）是一类重要的非编码RNA家族，具有重要的序列特异性转录后调控功能。识别miRNAs是理解转录后调控机制的重要要求。通过直接克隆和计算方法，已在几个物种中鉴定出数百种miRNA。然而，由于缺乏序列特征或强大的算法来有效地识别它们，仍然有许多miRNA有待识别。结果我们评估了对前体miRNA预测有价值的特征，例如miRNA茎区的局部二级结构差异和非miRNA发夹。我们还建立了不同类型的突变与pre-miRNAs二级结构之间的相关性。利用这些特点，结合当前pre-miRNA预测方法的一些改进，我们实现了一种计算学习方法SVM（supportvectormachine），构建了一个高通量、高性能的计算pre-miRNA预测工具MiRQs。该工具被设计用于两个相关物种的基因组、成对序列。该工具中内置的方法由两个主要步骤组成：1）发夹候选物的全基因组搜索和2）基于通过SVM方法对18个参数的分析排除非稳健结构。将该工具应用于鸡/人和D.黑腹果蝇D. pseudobscura成对基因组比对结果表明，该工具可用于全基因组pre-miRNA的预测。此工具位于 http://www.bioinformatics.org/mirfinder/ .
BackgroundMicroRNAs (miRNAs) are recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs is an important requirement for understanding the mechanisms of post-transcriptional regulation. Hundreds of miRNAs have been identified by direct cloning and computational approaches in several species. However, there are still many miRNAs that remain to be identified due to lack of either sequence features or robust algorithms to efficiently identify them.ResultsWe have evaluated features valuable for pre-miRNA prediction, such as the local secondary structure differences of the stem region of miRNA and non-miRNA hairpins. We have also established correlations between different types of mutations and the secondary structures of pre-miRNAs. Utilizing these features and combining some improvements of the current pre-miRNA prediction methods, we implemented a computational learning method SVM (support vector machine) to build a high throughput and good performance computational pre-miRNA prediction tool called MiRFinder. The tool was designed for genome-wise, pair-wise sequences from two related species. The method built into the tool consisted of two major steps: 1) genome wide search for hairpin candidates and 2) exclusion of the non-robust structures based on analysis of 18 parameters by the SVM method. Results from applying the tool for chicken/human and D. melanogaster/D. pseudoobscura pair-wise genome alignments showed that the tool can be used for genome wide pre-miRNA predictions.ConclusionThe MiRFinder can be a good alternative to current miRNA discovery software. This tool is available at http://www.bioinformatics.org/mirfinder/ .