Dotplot basics

A technique (Gibbs and McIntyre) for comparing sequences. All cogent3 sequence collections classes (SequenceCollection, Alignment) have a dotplot method.

The method returns a drawable, as demonstrated below between unaligned sequences.

If sequence names are not provided, two randomly chosen sequences are selected (see below). The plot title reflects the parameter values for defining a match. window is the size of the sequence segments being compared. threshold is the number of exact matches within window required for the two sequence segments to be considered a match. gap is the size of a gap between adjacent matches before merging.

Modifying the matching parameters

If we set window and threshold to be equal, this is equivalent to an exact match approach.

Displaying dotplot for the reverse complement

Note

clicking on an entry in the legend turns it off

Setting plot attributes

I’ll modify the title and figure width.