ss-count.pl - compute ss-count from a .ct file
ss-count.pl [OPTION]... file.ct [file.ext]
ss-count.pl computes the ss-count of each base for a set of structures in .ct format. The ss-count is the number of structures in which the base appears single-stranded.
The output from ss-count.pl is suitable for structure annotation with sir_graph.
If a .ext file is given, it is assumed to contain the correct probabilities. The output is expanded to include for each base the expected probability of being single-stranded, the standard deviation, the observed probability and the relative error (the observed probability minus the expected probability, divided by the standard deviation).
- -n, --normalized
- divides the ss-count for each base by the number of structures, to obtain a value in the range [0, 1]. Normalization is automatic when a .ext file is supplied.
- -w, --weighted
- computes a weighted sum or average, where the weights are the Boltzmann factors for each structure. Each Boltzmann factor is computed from a header line in the .ct file.
- -t, --temperature=temp
- sets the temperature for Boltzmann-weighting to temp. Default is 37.