BP_CHAOS_PLOT

NAME

chaos_plot − a chaos plot from DNA and RNA sequences

SYNOPSIS

  chaos_plot.pl −i/−−input=INPUTFILE −f/−−format=SEQFORMAT
        −o/−−output=OUTPUTFILE −g/−−graphics=GRAPHIC FORMAT
        −w/−−width=WIGHT −h/−−height=HEIGHT

DESCRIPTION

This scripts generates image files using GD image library to visualize nucleotide sequences using chaos plot.

OPTIONS

Valid graphics formats are currently gd, gd2, png, wbmp, jpeg and gif.

The default size of the image file is 600x400.

The sequence input can be provided using any of the three methods:
unnamed argument

  chaos_plot filename

named argument

  chaos_plot −i filename

standard input

  chaos_plot < filename

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl−l AT bioperl DOT org                  − General discussion
  http://bioperl.org/wiki/Mailing_lists  − About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.open−bio.org/

AUTHOR − Jason Stajich

Email jason AT bioperl DOT org

HISTORY

This code is based on EMBOSS C code for chaos.c by Ian Longden. Included are documentation from EMBOSS code:

Chaos produces a chaos plot. The original application is part of the ACEDB genome database package, written by ** Richard Durbin ( MRC LMB , UK ) rd@mrc−lmba.cam.ac.uk, and Jean Thierry-Mieg ( CRBM du CNRS , France) mieg AT crbm1 DOT cnusc DOT fr