QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis
QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis
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DOI：
10.1261/rna.036327.112
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发表时间：
2013-01-01
期刊：
影响因子：
4.5
通讯作者：
Weeks, Kevin M.
中科院分区：
文献类型：
--
作者：
Karabiber, Fethullah;McGinnis, Jennifer L.;Weeks, Kevin M.
RNA和DNA结构的化学探测是一种广泛使用的高信息量的方法，用于检测核酸结构和评估与蛋白质和小分子配体的相互作用。使用毛细管电泳来分析化学探测实验，每次实验产生数百个核苷酸的信息，可以在自动化仪器上进行。从毛细管电泳电泳图中提取信息是一个计算密集的多步骤分析过程，目前没有软件提供快速，自动化和准确的数据分析。为了克服这一瓶颈，我们开发了一个平台无关的，用户友好的软件包，QuShape，在最少的用户监督下产生定量准确的核苷酸反应性信息。QuShape结合了新开发的算法，用于信号衰减校正，在毛细血管内和毛细血管之间以及相对于RNA核苷酸序列的时变信号对齐，以及跨通道或实验的信号缩放。参考分析选项可以在几分钟内对多个相关实验进行全面分析。我们通过分析RNA SHAPE（引物延伸分析的选择性2’-羟基酰化）实验来说明QuShape的实用性和稳健性。
Chemical probing of RNA and DNA structure is a widely used and highly informative approach for examining nucleic acid structure and for evaluating interactions with protein and small-molecule ligands. Use of capillary electrophoresis to analyze chemical probing experiments yields hundreds of nucleotides of information per experiment and can be performed on automated instruments. Extraction of the information from capillary electrophoresis electropherograms is a computationally intensive multistep analytical process, and no current software provides rapid, automated, and accurate data analysis. To overcome this bottleneck, we developed a platform-independent, user-friendly software package, QuShape, that yields quantitatively accurate nucleotide reactivity information with minimal user supervision. QuShape incorporates newly developed algorithms for signal decay correction, alignment of time-varying signals within and across capillaries and relative to the RNA nucleotide sequence, and signal scaling across channels or experiments. An analysis-by-reference option enables multiple, related experiments to be fully analyzed in minutes. We illustrate the usefulness and robustness of QuShape by analysis of RNA SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experiments.