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Lirex： A Package for Identification of LongInverted Repeats in Genomes

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Genomics, Proteomics & Bioinformatics 2017年第2期15卷 141-146页

作者： Yong Wang Jiao-Mei Huang Institute of Deep-Sea Science and Engineering Chinese Academy of Sciences Sanya 572000 China

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.***.219.129/Lirex.

关键词： Lirex Inverted repeats Recombination stem-loop Mismatch rate

Expressional regulation in vitro of psbA mRNA 3' untranslated region in rice and sorghum

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Science China(Life Sciences) 1997年第4期40卷 406-413页

作者：钟珍萍吴乃虎 Institute of Developmental Biology Chinese Academy of Sciences Beijing 100080 China

To study the relationship between the structures of rice and sorghum psbA 3 UTR and gene expres-sional activity, six chimeric luc genes that encode luciferase under control of rice or sorghum psbA 5 UTR and 3’UTR or only 5 UTR were constructed. The levels of LUC accumulation in E . coli and the transcript stability in soluble pro-tein extracts of rice, sorghum chloroplast and E. coli were examined respectively, and a detailed analysis about the function of these two 3’UTR has been carried out. Here the regulation effect of these 3’UTR are reported: ( i ) When having the same promoter, the chimeric genes with rice 3 UTR produce LUC much more than that with sorghum 3 UTR; ( ii ) elimination of 3 UTR results in the fluctuation of LUC accumulation no matter whether it is under control of rice or sorghum psbA 5’UTR; ( Hi ) rice psbA 3’UTR exhibits a greater effect on stabilizing tran-scripts; ( IV ) psbA 3’lR-RNAs are more stable in chloroplast protein extracts than in E. coli protein extracts.

关键词： rice sorghum psbA 3’UTR stem-loop IR sequence regulation.

Identification of microRNA precursors with new sequence-structure features

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Journal of Biomedical Science and Engineering 2009年第8期2卷 626-631页

作者： Ying-Jie Zhao Qing-Shan Ni Zheng-Zhi Wang 不详

MicroRNAs are an important subclass of non-coding RNAs (ncRNA), and serve as main players into RNA interference (RNAi). Mature microRNA derived from stem-loop structure called precursor. Identification of precursor microRNA (pre-miRNA) is essential step to target microRNA in whole genome. The present work proposed 25 novel local features for identifying stem- loop structure of pre-miRNAs, which captures characteristics on both the sequence and structure. Firstly, we pulled the stem of hairpins and aligned the bases in bulges and internal loops used ‘―’, and then counted 24 base-pairs (‘AA’, ‘AU’, …, ‘―G’, except ‘――’) in pulled stem (formalized by length of pulled stem) as features vector of Support Vector Machine (SVM). Performances of three classifiers with our features and different kernels trained on human data were all superior to Triplet-SVM-classifier’s in po- sitive and negative testing data sets. Moreover, we achieved higher prediction accuracy through combining 7 global sequence-structure. The result indicates validity of novel local features.

关键词： MicroRNA Precursor MicroRNA Local Features Pulled stem stem-loop SVM

不同品种猪肌肉组织miR-1和miR-133基因的表达分析

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维普期刊数据库

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畜牧兽医学报 2012年第6期43卷 843-848页

作者：习欠云周莲莲李虹仪韩东束刚王松波高萍朱晓彤王修启江青艳张永亮华南农业大学动物科学学院广州510642 吉林大学畜牧兽医学院长春130062

本研究旨在探讨猪miR-1和miR-133基因在不同品种猪肌肉组织中的表达情况。试验以180日龄的蓝塘猪、长白猪以及大花白猪的背最长肌为材料,采用stem-loop实时定量RT-PCR法检测miR-1和miR-133在长白猪、大花白猪及蓝塘猪背最长肌组织中的... 详细信息

本研究旨在探讨猪miR-1和miR-133基因在不同品种猪肌肉组织中的表达情况。试验以180日龄的蓝塘猪、长白猪以及大花白猪的背最长肌为材料,采用stem-loop实时定量RT-PCR法检测miR-1和miR-133在长白猪、大花白猪及蓝塘猪背最长肌组织中的表达情况。结果表明,在蓝塘猪中,miR-1的表达量分别为长白猪和大花白猪的4.7和6.4倍,前者与后两者之间表达水平有显著的差异(P0.05);同样,miR-133在蓝塘猪中的表达量最高,其次为长白猪,两者分别是大花白猪的7.2和5.7倍,且差异显著(P0.05)。miR-1和miR-133在不同品种猪中存在特异性表达,提示可能与肌肉发育性状相关。

关键词： stem-loop RT-PCR 肉质性状 miR-1 miR-133 表达分析

miRNA qPCR检测方法研究进展及其应用

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生物技术通报 2016年第2期32卷 59-69页

作者：冯世鹏海南大学农学院海南省热带生物资源可持续利用重点实验室海口570228

miRNA是目前国际研究的热点领域之一,而miRNA表达检测是miRNA研究的基础内容。针对miRNA序列短小的特点,开发出了多种检测方法,其中miRNA qPCR定量检测是应用最广泛的方法。就miRNA抽提,miRNA qPCR定量检测原理及miRNA qPCR定量检测流... 详细信息

miRNA是目前国际研究的热点领域之一,而miRNA表达检测是miRNA研究的基础内容。针对miRNA序列短小的特点,开发出了多种检测方法,其中miRNA qPCR定量检测是应用最广泛的方法。就miRNA抽提,miRNA qPCR定量检测原理及miRNA qPCR定量检测流程包括引物设计、反应体系设置、内参基因筛选等方面进行了深入探讨,并对miRNA定量检测研究方法的发展趋势进行了展望,以期为研究者进行miRNA qPCR定量检测提供参考。

关键词： miRNA stem-loop RT-PCR poly(A)加尾法RT-PCR 延伸法RT-PCR 数字PCR