302 lines
13 KiB
Text
302 lines
13 KiB
Text
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Directory of files
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Suboptimal RNA folding package - M. Zuker, J. A. Jaeger, D. H. Turner
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Version 2.0
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Makefile - Standard UNIX makefile for RNA folding programs.
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alu.ct - A concatenation of 15 ct files containing part of the output
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produced by executing lrna using bat2.com as input.
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( lrna <bat2.com ) These are 15 foldings of an ALU
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sequence. The first is optimal.
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alu.distance - The output of the 'distance' program using alu.ct as
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input. This file contains all the pairwise distances
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between 15 different foldings of an ALU sequence.
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alu.out - Structure output file (120 record length) containing part of the
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output produced by running lrna using bat2.com as input. These
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are 15 foldings of an ALU sequence. The first is optimal.
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Selected base pairs are marked by |
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^ .
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alu.plot1 - This is an ASCII dot plot file created using
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the plot option in the energy dot plot mode. The run is
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a continuation using the alu.sav file. The energy
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increment selected is 114 ( 11.4 kcal/mole ) which is
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10% of the minimum computed free energy. 4 levels (or
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colors) were selected. The first level is for optimal
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base pairs. Levels 2, 3, and 4 correspond to energy
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increments of 3.8, 7.6, and 11.4 kcal/mole respectively.
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alu.plot2 - Similar to alu.plot1. Only three levels (colors) are used
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up to a total energy increment of 7.6 kcal/mole ( 6.6%
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from minimum ).
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alu.reg - A concatenation of 15 region files containing part of the ouput
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produced by running lrna using bat2.com as input. These are 15
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foldings of an ALU sequence. The first is optimal.
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alu.sav - The unformatted save file created by running lrna using
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bat1.com as input ( lrna <bat1.com ). This file can be
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used for a continuation run of lrna (as in : lrna <bat2.com).
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This file is for the folding of an ALU sequence using
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default energy files and no auxiliary information which would
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either force or prohibit specific base pairs.
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alu.seq - Sequence used in sample foldings. Note that A, C, G and U/T
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are in uppercase letters. Bases that are in lowercase
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letters will not be recognized by the program!
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alu.gcg - Output of figdot using alu.plot1 and alu.plot2 as input. The
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title is not included in this file. The figure program in the
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Genetics Computer Group package ( GCG ) can be used to transform
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this device independent plot file into a device specific plot
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file. The output is two energy dot plots for the folding of the
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ALU sequence ( produced from lrna using bat1.com & bat2.com ).
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You could also write your own program to create energy dot plots
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with labels and using multiple colors for different levels.
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bat1.com - Sample input file for folding an ALU sequence. This
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input file is the output of the batgen program and produces
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the save file alu1.sav.
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bat2.com - Sample input file for folding an ALU sequence. This
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command file is used as input to the lrna program. The
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save file, alu.sav, is read by lrna which then computes
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optimal and suboptimal foldings of an ALU sequence. Up
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to 200 foldings are allowed, although only 15 are generated.
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All foldings must be within 10% of the minimum computed free
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energy and the distance between any pair must be greater than 5.
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batgen - Executable code for batgen.
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batgen.f - Source code for batgen. This program creates input files for
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RNA folding.
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begin.dat - Author and reference information that are displayed
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before program execution.
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bpin.f - Source code for a subroutine used by distance.
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bpin.o - Object file for bpin.
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bpsrch.f - Source code for a subroutine used by distance.
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bpsrch.o - Object file for bpin.
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cdot.o - Object file for dotplot. Similar to ldot.o. This file is
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linked with others to create crna.
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circ.f - Source code for main; circular version of folding program.
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circ.inc - An include file for the circular version of the folding
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program. Note (see Makefile) that it is copied
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into a temporary file called rfd.inc (Rna FolDing).
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circ.o - Object file for rna.f for circular RNA folding.
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cmisc.o - Object file for mrna.f. This is similar to lmisc.o
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and is linked with others to create crna.
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crna - The circular verision of the RNA folding program (FORTRAN).
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crna.o - Object file for crna.
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csort.o - Object file for sort.f. Similar to lsort.o.
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cttobp - Executable file for cttobp.
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cttobp.f - Source code for a program that converts a ct file into
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a region and a sequence file, and vice versa.
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cttobp.o - Object file for cttobp.
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ct_gcg.f - This file contains an alternte for of the ct subroutine
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in mrna.f . This alternate generates ct files that
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can be read directly by GCG software.
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cvtct - Executable file for cvtct.
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cvtct.f - Source code for cvtct. This program converts a ct file into
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a .dat file used by the University of Wisconsin package
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for displaying RNA foldings (eg. SQUIGGLES accepts this
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file format). Needs jjlib.o at link time.
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cvtct.o - Object file for cvtct.
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dangle.dat - Energy file for single base stacking (dangling ends) at 37 deg.
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Entries marked "." should be interpreted as plus infinity.
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In such cases, no single base stacking occurs. Equivalent
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to dangle.037 .
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dangle.dh - Enthalpy file for single base stacking (dangling ends).
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This file is used by the newtemp program together with the
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dangle.dat file to produce energy files for folding at
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arbitrary temperatures between 0 and 100 deg. Some single
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base stacking energies may come out positive for high
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temperatures. The program only includes single base
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stacking if the energy increment is negative.
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Entries marked "." should be interpreted as plus infinity.
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distance - Executable file for distance.
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distance.f - Source code for distance. This program reads in a ct file
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containing between 2 and 15 structures and computes the
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distance between the first and all the rest or else the
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distance between all pairs.
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distance.o - Object file for distance.
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efn - Executable file for efn.
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efn.f - An independent program to compute the energies of foldings
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using a ct file as input. This program requires energy table
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input. The output consists of the computed energy of each
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folding found in the input ct file. Line printer output and/or
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region table output are options.
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efn.inc - Include file for efn. Needed when efn.f is compiled.
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errata2.list - List of errata found in version 2 folding programs
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with dates.
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figdot.doc - Documentation for figdot.
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figdot - Executable file for figdot.
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figdot.f - Source code for figdot. This program takes an ASCII plot
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file (produced by crna or lrna using the plot option
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in dotplt and converts it into a device inependent plot
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file for use by the FIGURE program from the Genetics
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Computer Group (GCG) package. The net result is to create
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an energy dot plot.
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files.list - This file.
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formid.f - Source code for formid. This subroutine reads and interprets
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sequence data.
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formid.o - Object file for formid. Linked to create both the linear and
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circular versions of the folding programs.
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getseq.f - Almost the same as formid.f. Used with batgen.
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getseq.o - Object file for getseq.
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jjlib.f - Some subroutines by John Jaeger that are needed by cvtct.
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jjlib.o - Object file for jjlib. Needed by cvtct at link time.
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lin.f - Source code for main; linear version of the folding program.
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lin.inc - An include file for the linear version of the folding
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program. Note (see Makefile) that it is copied
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into a temporary file called rfd.inc (Rna FolDing).
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lin.o - Object file for lin.
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lmisc.o - Object file for mrna.f. This is similar to cmisc.o and
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is linked with other files to create lrna.
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loop.dat - Energy data for hairpin, bulge and interior loops at 37 deg.
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Equivalent to loop.037
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lrna - Executable file for the linear version of the folding program.
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lrna.o - Object file for lrna.
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lsort.o - Object file for sort.f. Similar to csort.o.
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mfold.doc - A glossary of subroutines and functions used in the folding
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programs as well as a list of some of the varibles.
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mfold.flow - A flow chart for the main routine of the folding programs.
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mfold.user - A user's manual. Another description will appear :
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Predicting Optimal and Suboptimal Secondary Structure for RNA
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by J. A. Jaeger, D. H. Turner and M. Zuker, in
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"Molecular Evolution: Computer Analysis of Protein and
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Nucleic Acid Sequences", R. F. Doolittle ed.
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Methods in Enzymology, 183, 281-306, (1990).
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miscloop.dat - Miscellaneous loop file at 37 deg. Contains :
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i. a paramater for extrapolating bulge, interior and
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hairpin loop size beyond 30.
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ii. parameters for the Ninio "asymmetric interior loop"
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correction.
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iii. parameters used in computing the destabilizing effect
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of multi-branched loops.
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mrna.f - Miscellaneous subroutines for both the linear and circular
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versions of the folding program.
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multid.f - This subroutine reads and interprets sequence data. It
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differs from formid in that it automatically returns
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one sequence after another to the calling routine instead
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of requesting a sequence number of identifier.
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multid.o - Object file for multid. Linked to create both the linear and
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circular versions of the folding programs.
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newtemp - Executable file for newtemp.
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newtemp.f - Source code for newtemp. This program reads the 37 deg.
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energy files :
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stack.dat, tstack.dat, loop.dat, dangle.dat, tloop.dat
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& miscloop.dat
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as well as the enthalpy files :
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stack.dh, tstack.dh, dangle.dh & tloop.dh
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and computes new energy files for folding at any
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user defined temperature between 0 and 100 degrees.
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The output files are labelled with the appropriate
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temperature. For example, if 25 deg. is selected, the
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output energy files will be named :
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stack.025, tstack.025, loop.025, dangle.025, tloop.025
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& miscloop.025
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newtemp.o - Object file for newtemp.
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README - To be read first.
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rfd.inc - A temporary copy of either circ.inc or lin.inc.
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rna.f - FORTRAN source code (main)for RNA folding.
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sort.f - Source code for the sorting subroutines.
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stack.dat - Energy file for base pair stacking within helices at 37 deg.
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Entries marked "." should be interpreted as plus infinity.
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Equivalent to stack.037 .
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stack.dh - Enthalpy file for base pair stacking. This file
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is used by the newtemp program together with the stack.dat
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file to produce energy files for folding at arbitrary
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temperatures between 0 and 100 deg. Entries marked "."
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should be interpreted as plus infinity.
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tloop.dat - A list of distiguished tetraloops and the bonus energies
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given to them at 37 deg. These bonus energies are included
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in the final folding energies.
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Equivalent to tloop.037
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tloop.dh - Enthalpy file for distinguished tetraloops. This file
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is used by the newtemp program together with the tloop.dat
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file to produce bonus energies for listed tetraloops.
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tstack.dat - Energy file for terminal mismatched pairs in hairpin and
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interior loops at 37 deg. Entries marked "." should be
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interpreted as plus infinity. Equivalent to tstack.037 .
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tstack.dh - Enthalpy file for terminal mismatched pairs in hairpin and
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interior loops. This file is used by the
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newtemp program together with the tstack.dat file to
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produce energy files for folding at arbitrary
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temperatures between 0 and 100 deg. Entries marked "."
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should be interpreted as plus infinity.
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zsh - Zuker's shell : If you issue the command zsh 'name', a window
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will pop open called 'name' and the program 'name' will be
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run in that window. e.g. -- zsh lrna
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