
                               EMBOSS: chaos
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                                 Program chaos
                                       
Function

   Create a chaos game representation plot for a sequence
   
Description

   A box is drawn and an AGCT is drawn at each corner.
   
   Starting from the middle, move half way to the corner of the box
   representing the first base in the sequence and draw a dot.
   
   Then for each subsequent base move half way to the corresponding box
   corner and draw a dot.
   
   Finally display the number and percentage values of AGCT bases.
   
   The result is an image of a square sprinkled with dots. Areas which
   are devoid of dots (or heavily covered with dots) indicate short
   sequence motifs that are unusually infrequent (or frequent). The
   sequence of such motifs can be deduced by looking to see which quarter
   of teh square the region is in - the letter that this quarter belongs
   to is the first base of the motif. The quarter is then quartered again
   and the appropriate base letters are assigned to the corners of the
   quarter - the eigth part that the region is in gives the second base
   of the motif.
   
   The process continues until you have identified the 1/16th or 1/32nd,
   etc. of the original square containing the unusual region and you now
   have the sequence of the motif.
   
Usage

   Here is a sample session with chaos.
   
% chaos embl:eclac
Create a chaos game representation plot for a sequence
Graph type [x11]:

   click here for result
   
Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-sequence]          sequence   Sequence USA
*  -graph              graph      Graph type
*  -outfile            outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -data               bool       Display as data

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence USA Readable sequence Required
   -graph Graph type EMBOSS has a list of known devices, including
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png EMBOSS_GRAPHICS value, or x11
   -outfile Output file name Output file <sequence>.chaos
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -data Display as data Yes/No No
   
Input file format

   Any DNA sequence USA.
   
Output file format

   A graphics image is produced.
   
Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   0 upon successful completion.
   
Known bugs

   None.
   
See also

   Program name                          Description
   banana       Bending and curvature plot in B-DNA
   btwisted     Calculates the twisting in a B-DNA sequence
   compseq      Counts the composition of dimer/trimer/etc words in a sequence
   dan          Calculates DNA RNA/DNA melting temperature
   freak        Residue/base frequency table or plot
   isochore     Plots isochores in large DNA sequences
   wordcount    Counts words of a specified size in a DNA sequence
   
Author(s)

   This application was written by Ian Longden (il@sanger.ac.uk)
   Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus,
   Hinxton, Cambridge, CB10 1SA, UK.
   
History

 Completed 22nd March 1999.
 Last modified 14th June 1999.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
