Delila Program: exponential

# exponential program

## Pascal source code: exponential.p (wget instructions) Instructions on compiling Alphabetic List of Delila Programs Delila Programs by Most Recent Update Please report broken links Copyright Statement for Delila Programs

### 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 *)
(*
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

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}
```