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Prediction of Melting Profiles for Nucleic Acids

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Table of Contents

Name

ss-count.pl - compute ss-count from a .ct file

Synopsis

ss-count.pl [OPTION]... file.ct [file.ext]

Description

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).

Options

-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.

	Nicholas R. Markham Department of Computer Science	Michael Zuker Department of Mathematical Sciences
	Rensselaer Polytechnic Institute 2005-01-18