Delila Program: ridi

ridi program

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

{   version = 1.10; (* of ridi.p 2005 May 23}

(* begin module describe.ridi *)
(*
name
   ridi: Ri distribution prediction

synopsis
   ridi(ribl: in, ridip: in,
        data: out, sequ: out, output: out)

files

   ribl:  An individual information weight matrix created by the ri program.

   ridip:  parameters to control the program.  The file must contain the
      following parameters, one per line:

      parameterversion: The version number of the program.  This
         allows the user to be warned if an old parameter file is
         used.

      nrequest (integer): number of sequences to generate.  If it is
         less than 1, the number of sequences used to create the ribl
         will be used.  Aside from missing sequences on the edge, the
         resulting logo created from the sequence matches the natural
         logo in terms of small-sample error.

      seed (real): random number seed.  If seed < 0 or > 1 a timeseed
         is used.  A timeseed is created from the digits of the
         current date and time.  These digits are reversed and set
         behind the decimal point.  The resulting number is between 0
         and 1 and is used to start the random number generator.  The
         nice thing about a timeseed is that it will differ every time
         the program runs (as long as the runs are more than 1 second
         apart) and will not repeat for thousands of years.

      ricutoff (real): Lower bound for the individual information of a
         sequence for it to be accepted and printed.

   data: individual information predictions.  The first line is a
      comment, starting with '*'.  The remaining lines contain two
      columns.  The first column is the generated sequence (5' to
      3') and the second column is the Ri for that sequence
      evaluated by the original ribl matrix from file ribl

   sequ: individual sequences followed by a period.  This file can
      be used by makebk to create a delila book    and from there a
      sequence logo.  Be sure to use the z mode to set the zero
      base correctly.

   output: messages to the user

description

   Using the frequencies of bases at each position of a site (fbl
   matrix, carried in the ribl file) we use a random number generator
   to make up sequences that are similar to the original binding
   sites.  We can then evaluate those sequences to create a predicted
   Ri distribution.  The input of this program is an ribl matrix and
   the output is predicted information contents of randomly generated
   sequences that come from the fbl matrix.  If the program is
   repeatedly run, one can see how much the sequence logo varies for a
   given number of sequences.

examples

documentation

see also

   The program that computes the input ribl file is: ri.p

   The output is a data file that can be read by: genhis.p

   Program that can make a book from sequ: makebk.p

   Demonstration of jiggling logo:
   http://www.lecb.ncifcrf.gov/~toms/jigglogo/

   example parameter file: ridip

author

   Thomas Dana Schneider

bugs

technical notes

   If you make a movie be SURE that the time between ridi runs is at
   least 1 second so that the timeseed changes each time.  That is
   because the timeseed does not change more often than once per
   second.  If this is not done, sets of consecutive images will be
   identical.

*)
(* end module describe.ridi *)
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