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首页> 外文期刊>BMC Medical Genomics >MiteFinderII: a novel tool to identify miniature inverted-repeat transposable elements hidden in eukaryotic genomes
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MiteFinderII: a novel tool to identify miniature inverted-repeat transposable elements hidden in eukaryotic genomes

机译：MiteFinderII：鉴定真核生物基因组中隐藏的微型反向重复转座因子的新颖工具

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Miniature inverted-repeat transposable element (MITE) is a type of class II non-autonomous transposable element playing a crucial role in the process of evolution in biology. There is an urgent need to develop bioinformatics tools to effectively identify MITEs on a whole genome-wide scale. However, most of currently existing tools suffer from low ability to deal with large eukaryotic genomes. In this paper, we proposed a novel tool MiteFinderII, which was adapted from our previous algorithm MiteFinder, to efficiently detect MITEs from genomics sequences. It has six major steps: (1) build K-mer Index and search for inverted repeats; (2) filtration of inverted repeats with low complexity; (3) merger of inverted repeats; (4) filtration of candidates with low score; (5) selection of final MITE sequences; (6) selection of representative sequences. To test the performance, MiteFinderII and three other existing algorithms were applied to identify MITEs on the whole genome of oryza sativa. Results suggest that MiteFinderII outperforms existing popular tools in terms of both specificity and recall. Additionally, it is much faster and more memory-efficient than other tools in the detection. MiteFinderII is an accurate and effective tool to detect MITEs hidden in eukaryotic genomes. The source code is freely accessible at the website: https://github.com/screamer/miteFinder .
机译：微型反向重复转座因子（MITE）是II类非自主转座因子，在生物学的进化过程中起着至关重要的作用。迫切需要开发生物信息学工具，以在整个基因组范围内有效识别MITE。但是，目前大多数现有工具的处理能力均较弱，无法处理大型真核基因组。在本文中，我们提出了一种新颖的工具MiteFinderII，该工具是从以前的算法MiteFinder改编而来的，可以有效地从基因组序列中检测MITE。它包括六个主要步骤：（1）建立K-mer索引并搜索反向重复序列; （2）过滤反向重复序列，复杂度低; （3）反向重复的合并; （4）筛选低分的候选人; （5）选择最终的MITE序列; （6）代表性序列的选择。为了测试性能，将MiteFinderII和其他三个现有算法应用于在稻的整个基因组上鉴定MITE。结果表明，MiteFinderII在特异性和召回率方面均优于现有的流行工具。此外，它比检测中的其他工具快得多，存储效率更高。 MiteFinderII是检测隐藏在真核基因组中的MITE的准确有效的工具。可从以下网站免费访问源代码：https://github.com/screamer/miteFinder。

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