melt.pl

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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=RNA|DNA
sets nucleic acid type to RNA or DNA. Default is RNA.
-t, --temperature=temp
set temperature for energy minimization step to temp. Default is 37.
-N, --sodium=value
sets Sodium ion concentration to value molar. Default is 1.
-M, --magnesium=value
sets Magnesium ion concentration to value molar. Default is 0.
-C, --Ct=value
sets total strand concentration to value molar.
-p, --polymer
use salt corrections for polymers instead of oligomers (the default).
-I, --noisolate
prohibits 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=value
Bases farther apart than value cannot form. Default is no limit.
--circular
treats sequences as circular rather than linear. Only valid for folding.

Obscure Options

--allpairs
allows basepairs to form between any two nucleotides. When --allpairs is not specified, only Watson-Crick and wobble basepairs are allowed.
--maxloop=size
sets the maximum size of bulge/interior loops to size. Default is 30.
--nodangle
removes single-base stacking from consideration.
--simple
makes the penalty for multibranch loops constant rather than affine.
--prefilter=value1[,value2]
Sets 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).

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