How to use LBDotView:

1. Launch LBDotView by double clicking its icon.
2. Choose " File | Run lbdot " menu.
3. Enter parameters for lbdot (see below for explanation).
4. Click OK and wait for lbdot to generate dots.
5. When the dotplot appears, you may zoom in any region by dragging a rectangle.
6. You may undo zoom-in by double clicking the plot.
7. You may redo zoom-in by double clicking right mouse button 
   (holding Control key with MacOSX) on the plot. 


LBDot Parameters:

To generate a dotplot for sequences from two files, Filename1 and Filename2, 
you may simply enter:
Filename1 Filename2
then click OK. lbdot will generate a plot with default parameters. 


Format to specify parameters:
Filename1 Filename2 -twmrnop

where:
-t: type of sequence conversion
    0 - No conversion, direct comparison of two sequences
    1 - translation, comparison performed with translation code
    2 - TFT  (two for three) conversion, the first two letters out of three 
        used for coding
    What to use: use 0 for high eukaryote DNA sequences full of introns and 
                 un-translated regions, 1 and 2 for other cases. 2 is slightly 
                 more sensitive and takes more time. 

-w: window size

-m: Maximum mismatch allowed in a window.

-r: Repeats to ignore
    Highly repetitive sequences may slow down calculation. 
    Set this parameter, -r=10000, to ignore any repeat of >10000

-n: k-tuple of DNA sequence for fast comparison algorithm

-o: output file name of dotplot
    If not specified, Filename1-Filename2.ldt is used as dotplot file name.

-p: k-tuple of protein (or converted) sequence for fast comparison algorithm


Comments:

You may specify the type of conversion with -t parameter. For other parameters, 
it is recommended to use default values. If the generated dotplot is not 
sensitive enough, try to increase window size (-w) and mismatch (-m) values.



Examples with parameters:

Filename1 Filename2
   - Use all default parameters

Filename1 Filename2 -t=1
   - Use default parameters with Translation code for comparison

Filename1 Filename2 -w=60 -m=10 -r=12000
   - Use Window size of 60, Mismatch of 10 and ignoring repeats of >12000