NAME

hybrid-intra — hybridize two RNA or DNA sequences with intramolecular folding

SYNOPSIS

hybrid-intra [OPTION]... FILE1 FILE2

DESCRIPTION

hybrid-intra computes a partition function for the hybridization of the sequences in FILE1 and FILE2, allowing intramolecular basepairs to form. If the suffix option is used, the hybridization is computed using the energy rules with the suffix extension; otherwise, it is computed at each temperature from tMin to tMax degrees Celsius, in increments of tInc degrees. All output files are named with a prefix which consists of the first file name, a dash and the second file name, with the extension .seq removed from each file name. The partition function and associated free energy at each temperature are written to prefix.dG. The probabilities of each possible intermolecular basepair occurring are written to prefix.temperature.plot. A summary of the options the program was invoked with is written to prefix.run.

OPTIONS

-n, --NA=RNA2|RNA3|RNA|DNA: set nucleic acid type to RNA or DNA. Default is RNA.
-t, --tmin=REAL: set minimum temperature to REAL °C. Default is 0.
-i, --tinc=REAL: set temperature increment to REAL C°. Default is 1.
-T, --tmax=REAL: set maximum temperature to REAL °C. Default is 100.
-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).
-s, --suffix=STRING: use energy rules with the suffix STRING. Overrides --tmin, --tinc, --tmax, --sodium, --magnesium and --polymer.
-o, --output=STRING: name output files with the prefix STRING.
-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, force bases i to i+k-1 of the first sequence to be double-stranded; if i is 0, force bases j to j-k+1 of the second sequence to be double-stranded. k defaults to 1 if not specified.
--forceA=i,j[,k]: force all basepairs in the helix from i,j to i+k-1,j-k+1. If j is 0, force bases i to i+k-1 of the first sequence to be double-stranded; if i is 0, force bases j to j-k+1 of the first sequence to be double-stranded. k defaults to 1 if not specified.
--forceB=i,j[,k]: force all basepairs in the helix from i,j to i+k-1,j-k+1. If j is 0, force bases i to i+k-1 of the second sequence to be double-stranded; if i is 0, force 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.
--prohibitA=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 first sequence from pairing at all. k defaults to 1 if not specified.
--prohibitB=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 second 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.
--prohibit-rangeA=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 first sequence.
--prohibit-rangeB=i,j,k,l: prohibit any base from i to j of the second sequence from pairing with any base from k to l of the second sequence.
-E, --energy-only: skip computation of probabilities and output only prefix.dG and prefix.run. This mode uses less time and memory.
-k, --tracebacks=NUMBER: compute NUMBER stochastic tracebacks and write them to prefix.temperature.ct. Stochastic tracebacks are computed according to the Boltzmann probability distribution so that the probability of a structure is its Boltzmann factor divided by the partition function.
-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.
--constraintsA[=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 "--forceA=i,j,k", "--prohibitA=i,j,k" or "--prohibit-rangeA=i,j,k,l", respectively. If FILE is not specified, it defaults to prefix1.aux.
--constraintsB[=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 "--forceB=i,j,k", "--prohibitB=i,j,k" or "--prohibit-rangeB=i,j,k,l", respectively. If FILE is not specified, it defaults to prefix2.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.
--basepairsA=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.
--basepairsB=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.

OBSCURE OPTIONS

--allpairs: allow basepairs to form between any two nucleotides. When --allpairs is not specified, only Watson-Crick and wobble basepairs are allowed.
-d, --debug
--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.
--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.)
--nopostfilter: disable the postfilter. The postfilter, which is enabled by default, removes from consideration all structures that consist of only one basepair.
--scale=REAL: scale the partition function by the factor REAL per base.

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-intra 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

Both commercial and non-commercial use of UNAFold require a license from RPI; see https://ipo.rpi.edu/invention/unafold-version-40.