Delila Program: evd

evd program

Documentation for the evd program is below, with links to related programs in the "see also" section.

{   version = 2.53; (* of evd.p 2010 Sep 24}

(* begin module describe.evd *)
(*
name
   evd: evolution display

synopsis
   evd(all: in, evdp: in,
      display: out, sites: out, genomes: out, evfeatures: out,
      evdp: in, output: out);

files

   all: the all file from program ev.  It contains all the genomes of the
      evolving creatures, and other parameters and data.  It is created by a
      binary dump by the ev program for the sake of speed and so is not
      readable by people and so probably cannot be successfully run on
      another kind of computer.  The evd program therefore is needed to
      interpret the all file.

   evdp: parameters. one per line:

      firstcreature:   the number of the first creature to display

      secondcreature:  the number of the last creature to display

      non-site features:  if the first character is 'n' then non-sites
         that are recognized by the weight matrix are shown as features
         in evfeatures

      If evdp is empty, the defaults are: 1/1/- (first creature only,
      no non-site features)

      The creature of rank 1 makes the fewest mistakes;
      number 2 makes more, etc.

   display: a marked display of the genomes and other data.

   sites: raw sequences of the sites (and 5 bases around each), the sequences
      are separated by periods, and different creatures are separated by
      blank lines.  The current method for using this to create a sequence
      logo is described in the 'see also' section.

   genomes: raw sequences of the genomes of the creatures,
      separated by periods.

   evfeatures:  The features in this genome in the form used by the
      lister program.

   output: messages to the user.

description

   The purpose of the ev program is to evolve sites; the purpose of evd is to
   display an intermediate or final result of an evolutionary run.  The
   genomes are displayed with the locations of the recognizer gene and its
   sites:

      a-- c-- g-- t-- is the region encoding the weights for
                      one of the recognizer fingers.
                      The numbers underneath are the weights for each base.

      TTTT            marks the threshold for the matrix.
                      The number underneath is the threshold.

      (-------------) is a site.  The number underneath is the evaluation
                      of the site by the weight matrix.  If the site is
                      recognized (the evaluation is greater or equal
                      to the threshold) then + signs are used.

   The sequences around each site are written to the file 'sites', and the
   entire genomes are written to the file 'genomes'.  This allows analysis
   by other programs.

   EXPERIMENTAL: Thermodynamic Probabilities and Information of Weight Matrix

   Thermodynamic probabilities are computed by assuming that the weight
   matrix values represent energies, which may not be true.  However, given
   this assumption, we can compute the corresponding probabilities in a
   Boltzmann distribution by first computing the partition function Q = sum_b
   exp(weight_b) where b is one of the four bases and weight_b is the weight
   at some position l for base b.  Then the probability for base b is
   exp(weight_b)/Q.  The uncertainty and information are then computed in the
   normal way.  As a technical note, weight values are often high integers,
   such as 400.  This will exceed the capability of the exponentiation.  To
   avoid this, the absolute value of the weights at all positions are taken
   and the largest weight is used to normalize the entire matrix to the range
   -1 to +1.

   2002 April 4: The thermodynamic computation was implemented.  Notably, for
   the standard evp.selection at 1000 generations, where Rf = 4.0 and Rs =
   4.71035+/-0.29733, the computed value is 0.98 bits.  I do not yet know
   what this discrepancy means.  However, if the normalization is set to be
   between -0.5 and +0.5, then the computed value increases to 3.08 bits.
   This may indicate that the computation is meaningless or that something
   else has to be done ...

see also

   The "Evolution of Biological Information" paper (with active hypertext
   links in references): http://www-lecb.ncifcrf.gov/~toms/paper/ev/

   Example parameter file: evdp

   Program for the evolution of binding sites (this creates the all file):
   ev.p

   Program to display the genomes marked by the sites:
   * individual information version: lister.p
   * public version: listerx.p
   These programs require the Delila book format rather than the
   simple sequence in the genomes file.  To convert, use the
   makebk.p program:

   cp genomes sequ    # copy the sites file to the sequ file
   makebk < makebkp   # make the delila book with makebkp and makebk.p

   image for donor.pure TO MAKE LOGOS:
   Briefly, after running ev to evolve binding sites, use this evd.p
   program to get the binding site sequences.  Then copy the sites file to
   the sequ file and use the makebk.p program (preferably in automatic
   mode) to create a Delila book.  Then use standard delila system programs
   to create the logo, as described at
   http://www.lecb.ncifcrf.gov/~toms/delila.html.

   Assuming that you have all the necessary input files, in detail the
   procedure is:

   ev                 # evolve the creatures with ev.p
   evd                # make the display files with this program, evd.p
   cp sites sequ      # copy the sites file to the sequ file (a unix command)
   makebk < makebkp   # make the delila book with makebkp and makebk.p
   encode             # be sure to use the f mode in encodep with encode.p
   rseq               # compute information using the rseq.p program
   dalvec             # make the symvec using the dalvec.p program
   makelogo           # make the logo from the symvec with makelogo.p.

   Descriptions of the required input files are given in the documentation of
   each program and a general review is given in the paper
   http://www-lecb.ncifcrf.gov/~toms/paper/oxyr/.

   An example script that performs the steps above and also creates all the
   necessary input files is run.ev.

   A movie of binding site evolution created using these steps
   is at http://www.lecb.ncifcrf.gov/~toms/paper/ev/movie/

author

   Thomas Dana Schneider

bugs

   none known (well, actually it's full of them... ;-)

   Evd cannot handle non-random site placement in the display file because
   the drawing mechanism was not designed to do so.  The lister or listerx
   program has to be used.  A warning is provided to output.

technical notes

*)
(* end module describe.evd *)
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