Delila Program: exponential
#
exponential program

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

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**{version = 1.03; (* of exponential.p 2003 Aug 22}
(* begin module describe.exponential *)
(*
name
exponential: create an exponential curve for binding site separtions
synopsis
exponential(exponentialp: in, exponentialdata: out, output: out)
files
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.
description
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.
examples
documentation
see also
Use random numbers to simulate this process: spray.p
author
Thomas Dana Schneider
bugs
technical notes
*)
(* end module describe.exponential *)
{This manual page was created by makman 1.44}
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