
                               EMBOSS: dottup
     _________________________________________________________________
   
                                Program dottup
                                       
Function

   Displays a wordmatch dotplot of two sequences
   
Description

   A dotplot is a graphical representation of the regions of similarity
   between two sequences.
   
   The two sequences are placed on the axes of a rectangular image and
   (in the simplest forms of dotplot) wherever there is a similarity
   between the sequences a dot is placed on the image.
   
   Where the two sequences have substantial regions of similarity, many
   dots align to form diagonal lines. It is therefore possible to see at
   a glance where there are local regions of similarity as these will
   have long diagonal lines. It is also easy to see other features such
   as repeats (which form parallel diagonal lines), and insertions or
   deletions (which form breaks or discontinuities in the diagonal
   lines).
   
   dottup looks for places where words (tuples) of a specified length
   have an exact match in both sequences and draws a diagonal line over
   the position of these words. This is a fast, but not especially
   sensitive way of creating dotplots. It is an acceptable method for
   displaying regions of substantial similarity between two sequences.
   
   Using a longer word (tuple) size displays less random noise, runs
   extremely quickly, but is less sensitive. Shorter word sizes are more
   sensitive to shorter or fragmentary regions of similarity, but also
   display more random points of similarity (noise) and runs slower.
   
Usage

   Here is a sample session with dottup.

% dottup embl:eclac embl:eclaci -wordsize=6 -gtitle="eclaci vs eclac"

   click here for result
   
Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-sequencea]         sequence   Sequence USA
  [-sequenceb]         sequence   Sequence USA
   -wordsize           integer    Word size
*  -data               bool       Output the match data to a file instead of
                                  plotting it
*  -graph              graph      Graph type
*  -xygraph            xygraph    Graph type
*  -outfile            outfile    Output file name

   Optional qualifiers (* if not always prompted):
*  -[no]boxit          bool       Draw a box around dotplot

   Advanced qualifiers:
   -stretch            bool       Use non-proportional axes

   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
   [-sequencea]
   (Parameter 1) Sequence USA Readable sequence Required
   [-sequenceb]
   (Parameter 2) Sequence USA Readable sequence Required
   -wordsize Word size Integer 2 or more 10
   -data Output the match data to a file instead of plotting it Yes/No No
   -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
   -xygraph 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>.dottup
   Optional qualifiers Allowed values Default
   -[no]boxit Draw a box around dotplot Yes/No Yes
   Advanced qualifiers Allowed values Default
   -stretch Use non-proportional axes Yes/No No
   
Input file format

   Any two sequence USAs of the same type (DNA or protein).
   
Output file format

   An image is output to the resquested output device.
   
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
   dotmatcher   Displays a thresholded dotplot of two sequences
   dotpath      Displays a non-overlapping wordmatch dotplot of two sequences
   polydot      Displays all-against-all dotplots of a set of sequences
   
   dotmatcher, by comparison, moves a window of specified length up each
   diagonal and displays a line over the window if the sum of the
   comparisons (using a substitution matrix) exceeds a threshold. It is
   slower but much more sensitive.
   
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 24th March 1999.
   
Target users

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