NAME

hybrid-2s.pl — hybridize two RNA or DNA sequences

SYNOPSIS

hybrid-2s.pl [OPTION]... FILE1 FILE2

DESCRIPTION

hybrid-2s.pl computes a minimum energy hybridization of the sequences in FILE1 and FILE2 and evaulates its enthalpy and entropy. It then calculates the free energy at each temperature in a range and writes a .dG file. hybrid-2s.pl also makes a copy of the .ext file for each temperature, so that it can act as a replacement for hybrid, 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 of the first sequence to be double-stranded; if i is 0, forces bases j to j-k+1 of the second sequence 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 of the first sequence from pairing at all; if i is 0, prohibit bases j to j-k+1 of the second sequence 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 of the first sequence from pairing with any base from k to l of the second sequence.
-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.)
-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.
--temperature=REAL
set the temperature at which the minimum-energy hybridization 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=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.
--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-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

SEE ALSO

hybrid(1), hybrid-min(1), hybrid-ss-2s.pl(1), hybrid2-2s.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.