NAME

concentrations.pl, concentrations-same.pl — extract and normalize mole fractions

SYNOPSIS

concentrations.pl PREFIX.br concentrations-same.pl PREFIX

DESCRIPTION

concentrations.pl reads PREFIX.conc (written by concentration) and normalizes the concentrations of each species. The raw concentration of each species is divided by the sum of the concentrations so that the sum of A, B, AA, BB and AB is 1.

concentrations-same.pl reads a file written by concentration-same and writes PREFIX.A, PREFIX.Au, PREFIX.Af and PREFIX.AA.

It is recommended to use hybrid2.pl to run hybrid, hybrid-ss, concentration, concentrations.pl and ensemble-dg and ensemble-ext instead of running concentrations.pl directly.

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

concentration(1), concentration-same(1), hybrid2.pl(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.