QuShape is a comprehensive, platform-independent, user-friendly, and complete software package that enables efficient, reliable, highly automated, and accurate analysis of high-throughput capillary electrophoresis-detected nucleic acid chemical probing experiments.
In QuShape, rapid and efficient algorithms are implemented to yield objective nucleotide reactivity information with minimal user supervision. Capillary electrophoresis data from any class of nucleic acid reactivity probing experiment – including SHAPE, conventional, hydroxyl radical, and enzyme-based – can be analyzed.
QuShape is self-contained and runs under Windows, MacOS/X, and Linux. All tools and methods are implemented using Python. PyQt is used for designing the user interface; NumPy and SciPy to manipulate data and arrays; and Matplotlib, a Python 2D plotting library, to produce figures. All packages are open-source software. QuShape has an extensive help guide and user tutorial.
F. Karabiber, J.L. McGinnis, O.V. Favorov and K.M. Weeks, QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. RNA 19, 63–73 (2013). link pdf
C.W. Leonard, C.E. Hajdin, F. Karabiber, D.H. Mathews, O.V. Favorov, N.V. Dokholyan and K.M. Weeks, Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. Biochemistry 52, 588-595 (2013). link pdf