Delila Program: exponential

exponential program

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

{version = 1.03; (* of exponential.p 2003 Aug 22}

(* begin module describe.exponential *)
   exponential: create an exponential curve for binding site separtions

   exponential(exponentialp: in, exponentialdata: out, output: out)


   exponentialp:  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.

      G (integer): size of the genome.

      n (integer): number of sites on the genome.

      maxdist (integer): largest distance to compute

   exponentialdata:  The number of sites predicted at spacings from 1
      to maxdist.


   For a given genome of size G and a set of sites n,
   give the distribution of spacings between sites.

   let p = n/G be the probability of a Fis site at a base.
   let q = (1-p) be the probability that a Fis site is not at a base

   Then the probability of having two fis sites separated by
   a distance d is p(q^d)p = p^2(q^d).

   Therefore the number of fis sites separated by exactly
   a distance d with no others between is Gp^2((1-p)^d).

   This is equivalent to dropping n sites randomly into the range
   between 1 and G.  Sort these and compute the distances between
   them.  Tabulate the distribution of these distances.



see also

   Use random numbers to simulate this process:  spray.p


   Thomas Dana Schneider


technical notes

(* end module describe.exponential *)
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