
                              EMBOSS: polydot
     _________________________________________________________________
   
                                Program polydot
                                       
Function

   Displays all-against-all dotplots of a set of 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
   (subject to threshold conditions) 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.
   
   polydot compares all sequences in a set of sequences, draws a dotplot
   for each pair of sequences by marking where words (tuples) of a
   specified length have an exact match in both sequences and optionally
   reports all identical matches to feature files.
   
Usage

   Here is a sample session with polydot.
   
% polydot globin.fasta -gtitle="Polydot of globin.fasta"

   click here for result
   
Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-sequences]         seqset     File containing a sequence alignment
   -wordsize           integer    Word size
*  -graph              graph      Graph type
*  -outfile            outfile    Output file name

   Optional qualifiers:
   -[no]boxit          bool       Draw a box around each dotplot
   -dumpfeat           bool       Dump all matches as feature files
   -format             string     format to Dump out as
   -ext                string     Extension for feature file

   Advanced qualifiers:
   -data               bool       Output the match data to a file instead of
                                  plotting it
   -gap                integer    This specifies the size of the gap that is
                                  used to separate the individual dotplots in
                                  the display. The size is measured in
                                  residues, as displayed in the output.

   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
   [-sequences]
   (Parameter 1) File containing a sequence alignment Readable sequences
   Required
   -wordsize Word size Integer 2 or more 6
   -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>.polydot
   Optional qualifiers Allowed values Default
   -[no]boxit Draw a box around each dotplot Yes/No Yes
   -dumpfeat Dump all matches as feature files Yes/No No
   -format format to Dump out as Any string is accepted gff
   -ext Extension for feature file Any string is accepted gff
   Advanced qualifiers Allowed values Default
   -data Output the match data to a file instead of plotting it Yes/No No
   -gap This specifies the size of the gap that is used to separate the
   individual dotplots in the display. The size is measured in residues,
   as displayed in the output. Integer 0 or more 10
   
Input file format

   It reads in a set of nucleic or protein sequences.
   
   The sequences may or may not be aligned.
   
Output file format

   A graphical image is displayed.
   
Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   0 if successful.
   
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
   dottup       Displays a wordmatch dotplot of two sequences
   
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 2nd June 1999.

Target users

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