Wang Yong, Huang Jiao-Mei
Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
Genomics Proteomics Bioinformatics. 2017 Apr;15(2):141-146. doi: 10.1016/j.gpb.2017.01.005. Epub 2017 Apr 7.
Long inverted repeats (LIRs) are evolutionarily and functionally important structures in genomes because of their involvement in RNA interference, DNA recombination, and gene duplication. Identification of LIRs is highly complicated when mismatches and indels between the repeats are permitted. Long inverted repeat explorer (Lirex) was developed and introduced in this report. Written in Java, Lirex provides a user-friendly interface and allows users to specify LIR searching criteria, such as length of the region, as well as pattern and size of the repeats. Recombinogenic LIRs can be selected on the basis of mismatch rate and internal spacer size from identified LIRs. Lirex, as a cross-platform tool to identify LIRs in a genome, may assist in designing following experiments to explore the function of LIRs. Our tool can identify more LIRs than other LIR searching tools. Lirex is publicly available at http://124.16.219.129/Lirex.
长反向重复序列（LIRs）在基因组中具有重要的进化和功能意义，因为它们参与RNA干扰、DNA重组和基因复制。当允许重复序列之间存在错配和插入缺失时，LIRs的识别非常复杂。本报告中开发并引入了长反向重复序列探索器（Lirex）。Lirex用Java编写，提供了用户友好的界面，允许用户指定LIR搜索标准，如区域长度以及重复序列的模式和大小。可以根据错配率和内部间隔区大小从已识别的LIRs中选择重组LIRs。作为一种在基因组中识别LIRs的跨平台工具，Lirex可能有助于设计后续实验来探索LIRs的功能。我们的工具比其他LIR搜索工具能识别更多的LIRs。Lirex可在http://124.16.219.129/Lirex上公开获取。
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