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Prediction of Melting Profiles for Nucleic Acids

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Name

ct-energy - evaluate the energy of a .ct file

Synopsis

ct-energy [OPTION]... [FILE]...

Description

ct-energy evaluates the energy of each structure in each FILE, such as those produced by mfold or by hybrid-min or hybrid-ss-min. In its default mode it prints the energy of each structure followed by a carriage return (but see the --verbose option below).

When no FILE is specified, or if FILE is -, ct-energy reads standard input.

Options

-n, --NA=RNA|DNA

sets nucleic acid type to RNA or DNA. Default is RNA.

-t, --temperature=temp

sets temperature 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.

-p, --polymer

use salt corrections for polymers instead of oligomers (the default).

-s, --suffix=string

use energy rules with the suffix string. Overrides --temperature, --sodium, --magnesium and --polymer.

-v, --verbose

causes ct-energy to output detailed information about each loop in the structure. Specify twice for even more verbosity.

-L, --logarithmic

make penalty for multibranch loops logarithmic rather than linear.

-V, --Vienna

consider single-base stacking in "Vienna mode", in which a single-stranded base that may stack on an adjacent basepair must always do so. By default, two states are considered for each such base: dangling and not dangling.

Obscure Options

--nodangle

removes single-base stacking from consideration.

--simple

makes the penalty for multibranch loops constant rather than affine.

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. ct-energy 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).

See Also

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

Table of Contents

• Name
• Synopsis
• Description
• Options
• Obscure Options
• Environment
• See Also

	Nicholas R. Markham Department of Computer Science	Michael Zuker Department of Mathematical Sciences
	Rensselaer Polytechnic Institute 2005-01-18