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
- 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.
REFERENCES
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 http://www.unafold.org/Dinamelt/dinamelt-references.php
SEE ALSO
hybrid-ss-min(1), hybrid-min(1)
AUTHORS
Nick Markham <markham@alum.rpi.edu> and Michael Zuker <zukerm@alum.mit.edu>
COPYRIGHT
Copyright (c) 2006-2021, Rensselaer Polytechnic Institute.
AVAILABILITY
Both commercial and non-commercial use of UNAFold require a license from RPI; see https://ipo.rpi.edu/invention/unafold-version-40.