Editing Sequence alignment (section)

===Dot-matrix methods===
{{Main|Dot plot (bioinformatics)}}
{| style="float:right"
| [[File:Mup locus showing DNA repeats.jpg|thumb|200px|Self comparison of a part of a mouse strain genome. The dot-plot shows a patchwork of lines, demonstrating duplicated segments of DNA.]]
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{| style="float:right"
| [[Image:Zinc-finger-dot-plot.png|thumb|200px|A DNA [[Dot plot (bioinformatics)|dot plot]] of a [[human]] [[zinc finger]] [[transcription factor]] (GenBank ID NM_002383), showing regional [[self-similarity]]. The main diagonal represents the sequence's alignment with itself; lines off the main diagonal represent similar or repetitive patterns within the sequence. This is a typical example of a [[recurrence plot]].]]
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The dot-matrix approach, which implicitly produces a family of alignments for individual sequence regions, is qualitative and conceptually simple, though time-consuming to analyze on a large scale. In the absence of noise, it can be easy to visually identify certain sequence features—such as insertions, deletions, repeats, or [[inverted repeat]]s—from a dot-matrix plot. To construct a [[Dot plot (bioinformatics)|dot-matrix plot]], the two sequences are written along the top row and leftmost column of a two-dimensional [[matrix (mathematics)|matrix]] and a dot is placed at any point where the characters in the appropriate columns match—this is a typical [[recurrence plot]]. Some implementations vary the size or intensity of the dot depending on the degree of similarity of the two characters, to accommodate conservative substitutions. The dot plots of very closely related sequences will appear as a single line along the matrix's [[main diagonal]].

Problems with dot plots as an information display technique include: noise, lack of clarity, non-intuitiveness, difficulty extracting match summary statistics and match positions on the two sequences. There is also much wasted space where the match data is inherently duplicated across the diagonal and most of the actual area of the plot is taken up by either empty space or noise, and, finally, dot-plots are limited to two sequences. None of these limitations apply to Miropeats alignment diagrams but they have their own particular flaws.

Dot plots can also be used to assess repetitiveness in a single sequence. A sequence can be plotted against itself and regions that share significant similarities will appear as lines off the main diagonal. This effect occurs when a protein consists of multiple similar [[structural domain]]s.