NAME
ensemble-ext, ensemble-ext-same — compute extinction of an ensemble of species
SYNOPSIS
ensemble-ext [OPTION]... PREFIX1 PREFIX2.br ensemble-ext-same [OPTION]... PREFIX
DESCRIPTION
ensemble-ext computes the extinction of a two-sequence ensemble. The input to ensemble-ext consists of the outputs of running hybrid or hybrid-ss on each species, as well as the output of running concentration on the ensemble. ensemble-ext writes PREFIX1-PREFIX2.ens.ext which containts the extinction of the ensemble at each temperature. It also writes PREFIX1-PREFIX2.ens.TmExt1 and PREFIX1-PREFIX2.ens.TmExt2, which contain the inflection and halfway points of the extinction curve. Both are approximations of the melting temperature; the latter is preferred. The file PREFIX1-PREFIX2.ens.MaxExt contains the maximum possible extinction, i.e. the extinction if all bases were unpaired.
ensemble-ext-same operates in the same manner on a one-sequence ensemble, using the output from concentration-same.
It is recommended to use hybrid2.pl to run hybrid, hybrid-ss, concentration, concentrations.pl, ensemble-dg and ensemble-ext instead of running ensemble-ext directly.
OPTIONS
- -n, --NA=RNA2|RNA3|RNA|DNA
- set nucleic acid type to RNA or DNA. Default is RNA.
- -p, --points=NUMBER
- use NUMBER points on either side of each point when performing numerical differentiation to determine the inflection point. Default is 1.
- -x, --exclude=A|B|AA|BB
- exclude the specified species from consideration. May be used more than once, to exclude multiple species.
- -o, --output=STRING
- name output files with the prefix STRING.
OBSCURE OPTIONS
- --single
- only sum extinctions for each nucelotide, rather than for each dinucleotide.
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
hybrid(1), hybrid-ss(1), 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.