DottyPlotter  Version 1.0c
July 31 1989  Don Gilbert
("dottyplot.readme" added 8/2/89 by Spencer Yeh for BIONET distribution)


INTRODUCTION

Dotty Plotter is a tool for drawing dot matrix comparisons of sequences 
in molecular biology.  Dot plots are used to view all areas of homology 
between two nucleic acid or protein sequences.  Dot plots are useful for 
determining if there are one or more segments of similarity between 
sequences. 

This first release of Dotty Plot contains a minimum of features. I hope 
to improve Dotty Plotter's sequence size and memory limits, and add 
features. 

Speed of Dotty Plotter.
Times for 2000 x 2000 sequence comparison (Blue.Seq x BlueKsm.seq) with 
a 15:25 stringency:window, results in 2407 dots plotted.

	Mac SE/30     40.seconds
	Mac II        53.seconds
	Mac SE       230.seconds
	microVax II  229.seconds (GCG Compare program) 

The matching window and stringency are parameters which may be varied
by the user.  The screen plot may be enlarged or reduced to examine a
portion of the graphic in greater detail.  Presentation quality dot
matrix plots can then be printed out from the application, or the
plots may be saved to the clipboard for manipulation in other
programs.


CONTACT ADDRESS

Don Gilbert   
BioComputing Office
Biology Dept.
Indiana University,  Bloomington, IN 47405

email:  Bitnet:  GilbertD@IUBACS.bitnet   
        Internet:  GilbertD@Gold.Bacs.Indiana.Edu


SYSTEMS SUPPORTED

Mac Plus, SE, and Macintosh II. 


AVAILABILITY

This program is available by anonymous FTP from BIONET (net.bio.net) in 
the directory ~ftp/public/mac/dottyplot or, for BIONET subscribers only, 
by postal mail from the BIONET Lending Library.  If you are a BIONET 
subscriber and would like to receive the DottyPlotter diskette by mail, 
please send a stamped, self-addressed return envelope along with a 
formatted diskette (specify capacity) and your request to:

	BIONET Administrator
	BIONET/ IntelliGenetics, Inc.
	700 East El Camino Real, Suite 300
	Mountain View, CA  94040

	tel.:  (415) 962-7337

Don Gilbert will also distribute the program by e-mail or diskette if 
you contact him directly.  He requests that you send a formatted 
diskette.


SOURCE CODE

Not distributed.


PROGRAM FILES before extraction:

dottyplot.readme            This documentation file.
dottyplot.hqx               Binhexed archive file of the
                            Application, documentation, and test files.


PROGRAM FILES after extraction:

blue.seq                 test sequence
blueksm.seq              test.sequence
DottyDoc.text            Documentation in text format
DottyDoc.Word3           Documentation in MS Word 3 format
DottyDoc.WriteNow        Documentation in WriteNow format
DottyPlot                Application file
dros-ig-seq              test sequence
misc-fitch.seq           test sequences
readseq.p                Pascal source for input routine


DOCUMENTATION

Documentation in a number of formats is available in the DottyDoc.* 
files.  In addition the program has an internal help text with 
instructions for generating the plots.


DEARCHIVING THE PROGRAM

".hqx" files must be first un-BinHexed.  To do this, use the "Other"
menu within the StuffIt program to choose the "Decode BinHex File..."
option or use the BinHex program's "File" menu to choose the "Download
-> Application" option.

Once the dottyplot.hqx file is converted, it will be placed in a 
DottyPlot.ARC application file.  This is a self-extracting archive of 
the DottyPlot files which is started by double-clicking.


STARTING THE PROGRAM

Double-click the DottyPlot application icon  and then load sequence 
files using the "Open..." command in the File menu.