Directory of files

      Suboptimal RNA folding package - M. Zuker, J. A. Jaeger, D. H. Turner

                             Version 2.0

Makefile - Standard UNIX makefile for RNA folding programs.

alu.ct - A concatenation of 15 ct files containing part of the output 
         produced by executing lrna using bat2.com as input.
         ( lrna  <bat2.com   ) These are 15 foldings of an ALU 
         sequence. The first is optimal.

alu.distance - The output of the 'distance' program using alu.ct as 
               input. This file contains all the pairwise distances 
               between 15 different foldings of an ALU sequence.

alu.out - Structure output file (120 record length) containing part of the
          output produced by running lrna using bat2.com as input. These 
          are 15 foldings of an ALU sequence. The first is optimal.
          Selected base pairs are marked by   |
                                              ^ .

alu.plot1 - This is an ASCII dot plot file created using
            the plot option in the energy dot plot mode. The run is
            a continuation using the alu.sav file. The energy
            increment selected is 114 ( 11.4 kcal/mole ) which is
            10% of the minimum computed free energy. 4 levels (or
            colors) were selected. The first level is for optimal
            base pairs. Levels 2, 3, and 4 correspond to energy
            increments of 3.8, 7.6, and 11.4 kcal/mole respectively.

alu.plot2 - Similar to alu.plot1. Only three levels (colors) are used 
            up to a total energy increment of 7.6 kcal/mole ( 6.6% 
            from minimum ).

alu.reg - A concatenation of 15 region files containing part of the ouput 
          produced by running lrna using bat2.com as input. These are 15
          foldings of an ALU sequence. The first is optimal.

alu.sav - The unformatted save file created by running lrna using
          bat1.com as input ( lrna  <bat1.com ). This file can be 
          used for a continuation run of lrna (as in : lrna <bat2.com).
          This file is for the folding of an ALU sequence using
          default energy files and no auxiliary information which would
          either force or prohibit specific base pairs.

alu.seq  - Sequence used in sample foldings. Note that A, C, G and U/T
           are in uppercase letters. Bases that are in lowercase
           letters will not be recognized by the program!

alu.gcg - Output of figdot using alu.plot1 and alu.plot2 as input. The
          title is not included in this file. The figure program in the
          Genetics Computer Group package ( GCG ) can be used to transform 
          this device independent plot file into a device specific plot 
          file. The output is two energy dot plots for the folding of the 
          ALU sequence ( produced from lrna using bat1.com & bat2.com ). 
          You could also write your own program to create energy dot plots 
          with labels and using multiple colors for different levels. 

bat1.com - Sample input file for folding an ALU sequence. This 
           input file is the output of the batgen program and produces
           the save file alu1.sav.

bat2.com - Sample input file for folding an ALU sequence. This
           command file is used as input to the lrna program. The
           save file, alu.sav, is read by lrna which then computes
           optimal and suboptimal foldings of an ALU sequence. Up 
           to 200 foldings are allowed, although only 15 are generated. 
           All foldings must be within 10% of the minimum computed free 
           energy and the distance between any pair must be greater than 5.

batgen - Executable code for batgen.

batgen.f - Source code for batgen. This program creates input files for
           RNA folding.

begin.dat - Author and reference information that are displayed 
            before program execution.

bpin.f - Source code for a subroutine used by distance. 

bpin.o - Object file for bpin.

bpsrch.f - Source code for a subroutine used by distance.

bpsrch.o - Object file for bpin.

cdot.o - Object file for dotplot. Similar to ldot.o. This file is
         linked with others to create crna.

circ.f - Source code for main; circular version of folding program.

circ.inc - An include file for the circular version of the folding
           program. Note (see Makefile) that it is copied
           into a temporary file called rfd.inc (Rna FolDing).

circ.o - Object file for rna.f for circular RNA folding.

cmisc.o - Object file for mrna.f. This is similar to lmisc.o 
          and is linked with others to create crna.

crna - The circular verision of the RNA folding program (FORTRAN).

crna.o - Object file for crna.

csort.o - Object file for sort.f. Similar to lsort.o.

cttobp - Executable file for cttobp.

cttobp.f - Source code for a program that converts a ct file into
             a region and a sequence file, and vice versa. 

cttobp.o - Object file for cttobp.

ct_gcg.f - This file contains an alternte for of the ct subroutine
             in mrna.f . This alternate generates ct files that
             can be read directly by GCG software.

cvtct - Executable file for cvtct.

cvtct.f - Source code for cvtct. This program converts a ct file into
            a  .dat  file used by the University of Wisconsin package
            for displaying RNA foldings (eg. SQUIGGLES accepts this
            file format). Needs jjlib.o at link time.

cvtct.o - Object file for cvtct.

dangle.dat - Energy file for single base stacking (dangling ends) at 37 deg. 
             Entries marked "." should be interpreted as plus infinity.
             In such cases, no single base stacking occurs. Equivalent
             to dangle.037 .

dangle.dh - Enthalpy file for single base stacking (dangling ends). 
            This file is used by the newtemp program together with the
            dangle.dat file to produce energy files for folding at
            arbitrary temperatures between 0 and 100 deg. Some single
            base stacking energies may come out positive for high
            temperatures. The program only includes single base
            stacking if the energy increment is negative.
            Entries marked "." should be interpreted as plus infinity.

distance - Executable file for distance.

distance.f - Source code for distance. This program reads in a ct file
             containing between 2 and 15 structures and computes the
             distance between the first and all the rest or else the
             distance between all pairs.

distance.o - Object file for distance.

efn - Executable file for efn. 

efn.f - An independent program to compute the energies of foldings
          using a ct file as input. This program requires energy table
          input. The output consists of the computed energy of each
          folding found in the input ct file. Line printer output and/or
          region table output are options.

efn.inc  - Include file for efn. Needed when efn.f is compiled.

errata2.list - List of errata found in version 2 folding programs  
               with dates.

figdot.doc - Documentation for figdot.

figdot - Executable file for figdot.

figdot.f - Source code for figdot. This program takes an ASCII plot
           file (produced by crna or lrna using the plot option
             in dotplt and converts it into a device inependent plot
             file for use by the FIGURE program from the Genetics
             Computer Group (GCG) package. The net result is to create 
             an energy dot plot.

files.list - This file.

formid.f - Source code for formid. This subroutine reads and interprets
           sequence data.

formid.o - Object file for formid. Linked to create both the linear and
           circular versions of the folding programs.

getseq.f - Almost the same as formid.f. Used with batgen.

getseq.o - Object file for getseq.

jjlib.f - Some subroutines by John Jaeger that are needed by cvtct.

jjlib.o - Object file for jjlib. Needed by cvtct at link time.

lin.f - Source code for main; linear version of the folding program.

lin.inc - An include file for the linear version of the folding
          program. Note (see Makefile) that it is copied
          into a temporary file called rfd.inc (Rna FolDing).

lin.o - Object file for lin.

lmisc.o - Object file for mrna.f. This is similar to cmisc.o and
          is linked with other files to create lrna.

loop.dat - Energy data for hairpin, bulge and interior loops at 37 deg.
           Equivalent to loop.037

lrna - Executable file for the linear version of the folding program.

lrna.o - Object file for lrna.

lsort.o - Object file for sort.f. Similar to csort.o.

mfold.doc - A glossary of subroutines and functions used in the folding
            programs as well as a list of some of the varibles.

mfold.flow - A flow chart for the main routine of the folding programs.

mfold.user - A user's manual. Another description will appear :
             Predicting Optimal and Suboptimal Secondary Structure for RNA
             by J. A. Jaeger, D. H. Turner and M. Zuker, in
             "Molecular Evolution: Computer Analysis of Protein and 
             Nucleic Acid Sequences", R. F. Doolittle ed.
             Methods in Enzymology, 183, 281-306, (1990).

miscloop.dat - Miscellaneous loop file at 37 deg. Contains :
               i. a paramater for extrapolating bulge, interior and
                  hairpin loop size beyond 30.
              ii. parameters for the Ninio "asymmetric interior loop"
                  correction.
             iii. parameters used in computing the destabilizing effect
                  of multi-branched loops.

mrna.f - Miscellaneous subroutines for both the linear and circular
         versions of the folding program.

multid.f - This subroutine reads and interprets sequence data. It
           differs from formid in that it automatically returns
           one sequence after another to the calling routine instead
           of requesting a sequence number of identifier. 

multid.o - Object file for multid. Linked to create both the linear and
             circular versions of the folding programs.

newtemp - Executable file for newtemp.

newtemp.f - Source code for newtemp. This program reads the 37 deg.
            energy files :
            stack.dat, tstack.dat, loop.dat, dangle.dat, tloop.dat
            & miscloop.dat
            as well as the enthalpy files :
            stack.dh, tstack.dh, dangle.dh & tloop.dh 
            and computes new energy files for folding at any
            user defined temperature between 0 and 100 degrees.
            The output files are labelled with the appropriate
            temperature. For example, if 25 deg. is selected, the
            output energy files will be named :
            stack.025, tstack.025, loop.025, dangle.025, tloop.025
            & miscloop.025

newtemp.o - Object file for newtemp.

README - To be read first.

rfd.inc - A temporary copy of either circ.inc or lin.inc.

rna.f - FORTRAN source code (main)for RNA folding.

sort.f - Source code for the sorting subroutines.

stack.dat - Energy file for base pair stacking within helices at 37 deg.
            Entries marked "." should be interpreted as plus infinity.
            Equivalent to stack.037 .

stack.dh - Enthalpy file for base pair stacking. This file
           is used by the newtemp program together with the stack.dat
           file to produce energy files for folding at arbitrary
           temperatures between 0 and 100 deg. Entries marked "."
           should be interpreted as plus infinity. 

tloop.dat - A list of distiguished tetraloops and the bonus energies
            given to them at 37 deg. These bonus energies are included 
            in the final folding energies.
            Equivalent to tloop.037

tloop.dh - Enthalpy file for distinguished tetraloops. This file
           is used by the newtemp program together with the tloop.dat
           file to produce bonus energies for listed tetraloops.

tstack.dat - Energy file for terminal mismatched pairs in hairpin and
             interior loops at 37 deg. Entries marked "." should be 
             interpreted as plus infinity. Equivalent to tstack.037 .

tstack.dh - Enthalpy file for terminal mismatched pairs in hairpin and
            interior loops. This file is used by the
            newtemp program together with the tstack.dat file to
            produce energy files for folding at arbitrary
            temperatures between 0 and 100 deg. Entries marked "."
            should be interpreted as plus infinity. 

zsh - Zuker's shell : If you issue the command  zsh 'name', a window
      will pop open called 'name' and the program 'name' will be
      run in that window. e.g. -- zsh lrna