| ## 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