NAME

hybrid-ss-2s.pl — fold an RNA or DNA sequence

SYNOPSIS

hybrid-ss-2s.pl [OPTION]... FILE

DESCRIPTION

hybrid-ss-2s.pl computes a minimum energy folding of the sequence(s) in FILE using hybrid-ss-min and evaulates its enthalpy and entropy. It then calculates the free energy at each temperature in a range and writes a .dG file. hybrid-ss-2s.pl also makes a copy of the .ext file for each temperature, so that it can act as a replacement for hybrid-ss, for example in hybrid2.pl.

OPTIONS

-n, --NA=RNA2|RNA|DNA: set nucleic acid type to RNA or DNA. Default is RNA.
-t, --tmin=REAL: set minimum temperature to REAL °C. Default is 37.
-i, --tinc=REAL: set temperature increment to REAL C°. Default is 1.
-T, --tmax=REAL: set maximum temperature 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.
-p, --polymer: use salt corrections for polymers instead of oligomers (the default).
-f, --force=i,j[,k]: force all basepairs in the helix from i,j to i+k-1,j-k+1. If j is 0, forces bases i to i+k-1 to be double-stranded; if i is 0, forces bases j to j-k+1 to be double-stranded. k defaults to 1 if not specified.
-r, --prohibit=i,j[,k]: prohibit all basepairs in the helix from i,j to i+k-1,j-k+1. If j is 0, prohibit bases i to i+k-1 from pairing at all; if i is 0, prohibit bases j to j-k+1 from pairing at all. k defaults to 1 if not specified.
-R, --prohibit-range=i,j,k,l: prohibit any base from i to j from pairing with any base from k to l.
-E, --energyOnly: skip computation of probabilities and output only prefix.dG and prefix.run.
-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 and --nopostfilter options below.)
-m, --maxbp=NUMBER: bases farther apart than NUMBER cannot form. Default is no limit.
-c, --constraints=FILE: read a list of constraints from FILE. Constraints must be in the form "F i j k", "P i j k" or "R i-j k-l". These are equivalent to specifying "--force=i,j,k", "--prohibit=i,j,k" or "--prohibit-range=i,j,k,l", respectively. If FILE is not specified, it defaults to prefix.aux.
-b, --basepairs=FILE: read a list of allowable helices from FILE. Each helix consists of three whitespace-delimited numbers which specify the starting basepair and the length of the helix. When this option is used, all basepairs except those in FILE are prohibited from forming.
--circular: treat sequences as circular rather than linear.
--temperature=REAL: set the temperature at which the minimum-energy folding is computed. Default is 37.

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=size: set the maximum size of bulge/interior loops to size. Default is 30.
--maxas=asym: set the maximum asymmetry of bulge/interior loops to asym. 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. hybrid-ss-2s.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.