psSHAPER - pseudo-SHAPE generator

psSHAPEr is a tool that converts RNA structural ensemble data into pseudo-SHAPE reactivity scores.

Overview

The tool takes either a DBN file (dot-bracket notation ensemble) or a BPP file (base pairing probability matrix) and converts it to pseudo-SHAPE reactivity values using a weighted consensus approach.

Input Formats

DBN format: A file containing multiple dot-bracket structures, one per line. Each line represents a predicted structure from an ensemble.

BPP format: A matrix file where each row corresponds to a nucleotide position, and columns contain pairing probabilities with other positions. The sum of probabilities for each row should be ≤ 1.
NOTE: Matrix format must have only values (no col or row titles) separated by either a TAB or a SINGLE space.
A typical example would be a bpp matrix as in output from Arnie (python wrapper), as:
0.000 0.000 0.0011 0.0118 0.2536
0.000 1.000 0.000 0.0241 0.000
0.0011 0.000 0.000 0.000 0.000
0.0118 0.0241 0.000 0.000 0.3112
0.2536 0.000 0.000 0.3112 0.000

Parameters

• x1, x2, x3: Threshold values for consensus ranges (default: 0.9, 0.5, 0.3)
• k1, k2, k3: Weight multipliers for each consensus range (default: 2, 1.25, 0.75)

Output

The tool generates a shape.dat file containing position-indexed pseudo-SHAPE reactivity scores, formatted as: position score (one per line).

Additionally, an interactive plot shape_plot.html is generated showing the values with threshold lines.