NAME

melt.pl — compute entropy and melting temperature for a two-state model

SYNOPSIS

melt.pl [OPTION]... FILE [FILE]

DESCRIPTION

melt.pl performs two-state folding or hybridization calculations. If one FILE is given, a minimum energy folding is computed for each sequence in the file using hybrid-ss-min; if two FILEs are given, a minimum energy hybridization is computed for each pair of sequences using hybrid-min. In either case, the free energy, enthalpy, entropy and melting temperature are written to standard output for each calculation.

For hybridization calculations, the total strand concentration must be specified with the --Ct option.

OPTIONS

-n, --NA=RNA2|RNA|DNA: set nucleic acid type to RNA or DNA. Default is RNA.
-t, --temperature=REAL: set temperature for energy minimization step to REAL °C. Default is 37.
-N, --sodium=REAL: set Sodium ion concentration to REAL molar. Default is 1.
-M, --magnesium=REAL: set Magnesium ion concentration to REAL molar. Default is 0.
-C, --Ct=REAL: set total strand concentration to REAL molar.
-p, --polymer: use salt corrections for polymers instead of oligomers (the default).
-I, --noisolate: prohibit all isolated basepairs. Isolated basepairs are helices of length 1; that is, they do not stack on another basepair on either side. (See also the --prefilter option below.)
-m, --maxbp=NUMBER: bases farther apart than NUMBER cannot form. Default is no limit.
--circular: treat sequences as circular rather than linear. Only valid for folding.

OBSCURE OPTIONS

--allpairs: allow basepairs to form between any two nucleotides. When --allpairs is not specified, only Watson-Crick and wobble basepairs are allowed.
--maxloop=NUMBER: set the maximum size of bulge/interior loops to NUMBER. Default is 30.
--maxas=NUMBER: set the maximum asymmetry of bulge/interior loops to NUMBER. Default is 30.
--nodangle: remove single-base stacking from consideration.
--simple: make the penalty for multibranch loops constant rather than affine.
--prefilter=value1[,value2]: set the prefilter to filter out all basepairs except those in groups of value2 adjacent basepairs of which value1 can form. value2 is the same as value1 if unspecified. Default is 2 of 2. (See also the --noisolate option above.)

ENVIRONMENT

UNAFOLDDAT: an alternate location from which to read the energy rules. The default energy rules can be overridden with files in the current directory or in the directory pointed to by UNAFOLDDAT. melt.pl looks for each file first in the current directory, then in the directory specified by UNAFOLDDAT and last in /usr/local/share/unafold (or wherever the energy rules were installed).

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

AUTHORS

Nick Markham <markham@alum.rpi.edu> and Michael Zuker <zukerm@alum.mit.edu>

COPYRIGHT

AVAILABILITY

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.