NAME — compute h-num from a .plot file


DESCRIPTION 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


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


Nick Markham <> and Michael Zuker <>


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Both commercial and non-commercial use of UNAFold require a license from RPI; see