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# 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.