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dottup |
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.
% dottup embl:eclac embl:eclaci -wordsize=6 -gtitle="eclaci vs eclac"click here for result
Mandatory qualifiers (* if not always prompted): [-sequencea] sequence Sequence USA [-sequenceb] sequence Sequence USA -wordsize integer Word size * -data boolean 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 boolean Draw a box around dotplot Advanced qualifiers: -stretch boolean Use non-proportional axes General qualifiers: -help boolean 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 |
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.