The DINAMelt Server
Prediction of Melting Profiles for Nucleic Acids
References Download the UNAFold software Commercial license Contact us Server home
Table of Contents
hybrid-ss-2s.pl - fold an RNA or DNA sequence
hybrid-ss-2s.pl [OPTION]... FILE
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.
- -n, --NA=RNA|DNA
- sets nucleic acid type to RNA or DNA. Default is RNA.
- -t, --tmin=temp
- sets minimum temperature to temp. Default is 37.
- -i, --tinc=temp
- sets temperature increment to temp. Default is 1.
- -T, --tmax=temp
- sets maximum 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).
- -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.
- -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.
- -E, --energyOnly
- skips computation of probabilities and outputs only prefix.dG and prefix.run.
- -I, --noisolate
- prohibits 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=value
- Bases farther apart than value cannot form. Default is no limit.
- -c, --constraints=file
- reads a list of constraints from file. Constraints must be in the form "P i j k" or "F i j k". These are equivalent to specifying "--prohibit=i,j,k" and "--force=i,j,k", respectively. If file is not specified, it defaults to prefix.aux.
- -b, --basepairs=file
- reads 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=temp
- sets the temperature at which the minimum-energy folding is computed. Default is 37.
- --allpairs
- allows basepairs to form between any two nucleotides. When --allpairs is not specified, only Watson-Crick and wobble basepairs are allowed.
- --maxloop=size
- sets the maximum size of bulge/interior loops to size. Default is 30.
- --nodangle
- removes single-base stacking from consideration.
- --simple
- makes the penalty for multibranch loops constant rather than affine.
- --prefilter=value1[,value2]
- Sets 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.)
- 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).
hybrid-ss(1), hybrid-ss-min(1), hybrid-2s.pl(1), hybrid2-2s.pl(1)
 |
Nicholas R. Markham
Department of Computer Science |
Michael Zuker
Department of Mathematical Sciences |
Rensselaer Polytechnic Institute
2005-01-18 |