h-num.pl — compute h-num from a .plot file
h-num.pl computes the h-num of each helix in an energy dot plot prefix.plot and writes it to prefix.h-num.
hybrid-ss-min and hybrid-min calculate p-num values for each base; the p-num value is the number of pairing partners the base can have. The h-num for a particular base pair is defined as the sum of the p-num values for each base minus one, and the h-num for a helix is the average of the h-num values of each base pair in the helix.
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
Nick Markham <email@example.com> and Michael Zuker <firstname.lastname@example.org>
Copyright (c) 2006-2021, Rensselaer Polytechnic Institute.
UNAFold is available from http://www.unafold.org/Dinamelt/software/obtaining-unafold.php. Commercial use requires a license; see https://ipo.rpi.edu/invention/unafold-version-40.