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EMBOSS: polydot |
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.
% polydot globin.fasta -gtitle="Polydot of globin.fasta"
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 |
The sequences may or may not be aligned.
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 |
Completed 2nd June 1999.