Delila Program: winrs

winrs program

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

{version = 1.16; (* of winrs.p 1996 April 10}

(* begin module describe.winrs *)
(*
name
   winrs: Compute Rs/window vs window in a single program

synopsis
   winrs(book: in, cmp: in, winrsp: in, xyin: out, output: out)

files
   book: A book from Delila.  Only the first DNA piece in the book is used.

   cmp: A composition from the comp program.
       If cmp is empty, then equal frequencies are assumed.

   winrsp:  :  Parameters to control the program: one per line

      StartCoordinate (integer):  The base of the sequence to be used for the
         zero coordinate of the first window.  For simplicity, internal
         coordinates are used: the sequence begins at base 1.

      MinimumWindowSize (integer): The shortest window to use for the
         computations.

      MaximumWindowSize (integer): The longest window to use for the
         computations.

      SpaceBetweenWindows (integer):  Windows are spaced so as to not
         collide.  You can add extra distance with this parameter.
         If it is negative, the windows will overlap.

      NumberofWindows (integer): The number of windows to use for
         each computation.

      * The program will object if any of these parameters cause a window to
      go outside the sequence.

   xyin: output of this program, input to the xyplo graphics program.
         columns:
         1: window size
         2: Rs, Rsequence, bits
         3: SD, Standard Deviation of Rs, bits
         4: Rs/(window size), bits/base
         5: SD/(window size), bits/base

   output: messages to the user

description

   A window size is chosen.  The first sequence in the book is broken into
   fragments of this size.  These are aligned and the information content,
   Rsequence (Rs) is computed.  This process is repeated for a range of
   window sizes defined in the parameters.  The output is a data file (xyin)
   containing columns for window size (w), Rs and the standard deviation of
   Rs (SD).  There are also two normalized columns for Rs/w and SD/w, which
   are reports in bits per base.  Repeating structures will appear as peaks
   in a graph of Rs/w versus w.

examples

documentation
   [1996 April 8]

see also
   lidel.p, winscan.p, delila.p, encode.p, rseq.p, xyplo.p

author
   Thomas Dana Schneider

bugs
   The program should produce a xyplop so that it can put
   the genomic information on the curve automatically.

technical notes
   Paremeter dnamax must be set as large as possible so that the entire
   sequence can fit into a single array and therefore be accessed as rapidly
   as possible.  Since Delila stores sequences with 2 bits/base (assuming a
   good compiler) so one can compute the size of the array in bytes.

*)
(* end module describe.winrs *)
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