Written by Tiyaporn Tangpradabkul (October 30, 2023)
This GitHub repository contains following folders:
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hitrace: MATLAB scripts used for analyzing SHAPE reactivities of WT mini-PTC, seven Eterna mini-PTC designs, WT mini-PTC with A- and P-site analogs, mini-PTC 1.1 with A- and P-site analogs. Raw capillary electrophoresis data is uploaded as "ce_data.zip" in the supplementary files.
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ribopaint: TIFF files and MATLAB scripts used to plot SHAPE reactivities on figures.
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python_scripts: This folder is seperated into two folders. Heatmap folder contains .txt files that show experimental SHAPE reactivities of all mini-PTC constructs and predicted SHAPE reactivity of WT mini-PTC. In addition, a python script used to generate a heatmap that summarizes SHAPE reactivity of mini-PTC constructs is also included. wt_distribution folder contains .txt files that indicate differential SHAPE reactivity between experimental and predicted WT mini-PTC construct and a python script used to generate a distribution plot and identify extreme outliers according to 3 x IQR rule.
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saved_hitrace_workspace: Saved processed data after analyzing SHAPE reactivity using data and scripts in the Hitrace folder. These includes data of WT mini-PTC, seven Eterna PTC designs, WT mini-PTC with A- and P-site analogs, mini-PTC 1.1 with A- and P-site analogs.
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saved_ribopaint_workspace: Saved processed data after plotting SHAPE reactivities on the figures using data and scripts in the Hitrace folder. These includes data of WT mini-PTC, seven Eterna PTC designs, WT mini-PTC with A- and P-site analogs, mini-PTC 1.1 with A- and P-site analogs.
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MATLAB scripts in this repository were run using MATLAB 2022a version with the following installed toolboxes:
- Optimization Toolbox version 9.3
- Signal Processing Toolbox version 9.0
- Image Processing Toolbox version 11.5
- Mapping Toolbox version 5.3
- Statistics and Machine learning Toolbox version 12.3
- Bioinformatics Toolbox version 4.16
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Hitrace and Ribopaint MATLAB packages can be downloaded ans installed from https://github.com/ribokit/HiTRACE and https://github.com/ribokit/RiboPaint
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Python scripts in this repository assume a Python 3 environment. A Fitter package can be downloaded from https://fitter.readthedocs.io/en/latest/