NAME — compute ss-count from a .ct file

SYNOPSIS [OPTION]... file.ct [file.ext]

DESCRIPTION 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 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
divide 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
compute 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=REAL
set the temperature for Boltzmann-weighting to REAL °C. Default is 37.


Markham, N. R. and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization. In Keith, J. M., editor, Bioinformatics, Volume II. Structure, Functions and Applications, number 453 in Methods in Molecular Biology, chapter 1, pages 3-31. Humana Press, Totowa, NJ. ISBN 978-1-60327-428-9.

Other references which may be useful may be found at


hybrid-ss-min(1), hybrid-min(1)


Nick Markham <> and Michael Zuker <>


Copyright (c) 2006-2021, Rensselaer Polytechnic Institute.


UNAFold is available from Commercial use requires a license; see