Delila Program: chaos

chaos program

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

{version = 1.05; (* of chaos.p 1996 October 21}

(* begin module describe.chaos *)
(*
name
   chaos: chaotic analysis of scan data

synopsis
   chaos(data: in, xyin: out, output: out)

files
   data:  data from the scan program

   xyin:  data rearranged for chaotic analysis plot.  The file
      format is ready for input to xyplo.

   output: messages to the user

description
   A "classical" test for chaos in a system is to transform the series:
     x1, x2, x3, x4, x5, ...
   Into a set of pairs of coordinates:
     (x1,x2)
     (x2,x3)
     (x3,x4)
     (x4,x5)
     ...
   If there is no relationship, then one gets a random-looking
   scatter diagram.  If there is a chaotic relationship, one gets
   curves.

   This program uses the potential locations of binding sites found
   by the scan program (and output in file 'data') as the input series.
   These values are then weighted by their probability.

examples

   data:

* DEFINITION OF THE DATA COLUMNS:
* 1 piece number
* 2 piece length
* 3 piece name
* 4 piece coordinate
* 5 matrix orientation (+1 = as in book, -1 = complement)
* 6 Ri evaluation (bits per site)
* 7 Z
* 8 probability
*
    1  87192 p1                     15    1     2.184500    -2.223394     0.013095
    1  87192 p1                     81    1     1.000218    -2.648260     0.004045
    1  87192 p1                     88    1     2.780186    -2.009690     0.022232
    1  87192 p1                    109    1     5.395104    -1.071578     0.141955
    1  87192 p1                    113    1     1.761704    -2.375074     0.008773
    1  87192 p1                    165    1     1.217743    -2.570222     0.005082
    1  87192 p1                    387    1     3.648239    -1.698272     0.044728
    1  87192 p1                    447    1     1.022737    -2.640181     0.004143
    1  87192 p1                    480    1     2.553458    -2.091029     0.018263
    1  87192 p1                    528    1     6.956904    -0.511276     0.304579
    1  87192 p1                    540    1     2.927385    -1.956881     0.025181
    1  87192 p1                    587    1     1.316462    -2.534806     0.005625
    1  87192 p1                    609    1     6.937751    -0.518147     0.302178
    1  87192 p1                    621    1     1.241720    -2.561620     0.005209
    1  87192 p1                    625    1     2.097234    -2.254701     0.012076
    1  87192 p1                    705    1     1.965286    -2.302038     0.010667
    1  87192 p1                    992    1     3.166391    -1.871137     0.030663
    1  87192 p1                   1108    1     1.757896    -2.376440     0.008740

documentation

see also
   scan.p, xyplo.p

author
   Thomas Dana Schneider

bugs

   The program uses the coordinates reported in the data file.  Since these are
   piece coordinates they are not necessarily linear (ie, 1 to n).  If
   fragments have been extracted from a circular sequence, the results will
   have some incorrect data.  (This is a minor bug.)

technical notes

*)
(* end module describe.chaos *)
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