Using nipype for mfe calculation of p7308 sub-sequences.

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Using nipype for mfe calculation of p7308 sub-sequences.

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Last edited Nov 27, 2013

Created on Nov 23, 2013

This example visualizes the distribution of mean free energy (ΔG) values for overlapping 500-base-pair sub-sequences of the p7308 genome. The notebook computes these values using NuPack’s mfe binary through a Nipype pipeline, then plots a histogram of the results with matplotlib and prettyplotlib. The code extracts ΔG values from text output files and displays the histogram with 30 bins, labeled axes, and a title indicating the sequence length and temperature.

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deltaG p7308 calculations

A histogram displays the distribution of calculated free-energy values (ΔG) for 500-base-pair subsequences of the p7308 genome, with results extracted from NuPack’s minimum free energy (mfe) output files. The plot uses matplotlib via prettyplotlib to render 30 bins, labeling axes with ΔG and sequence count, and titles the figure with the temperature condition. The underlying pipeline processed 7,308 subsequences, as indicated by the file count and extraction function.

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