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DOTTUP application details page
Displays a wordmatch dotplot of two sequences
A dotplot is a graphical representation of the regions of similaritybetween two sequences. The two sequences are placed on the axes of a rectangular image and(in the simplest forms of dotplot) wherever there is a similaritybetween the sequences a dot is placed on the image. Where the two sequences have substantial regions of similarity, manydots align to form diagonal lines. It is therefore possible to see at aglance where there are local regions of similarity as these will havelong diagonal lines. It is also easy to see other features such asrepeats (which form parallel diagonal lines), and insertions ordeletions (which form breaks or discontinuities in the diagonal lines). dottup looks for places where words (tuples) of a specifiedlength have an exact match in both sequences and draws a diagonal lineover the position of these words. This is a fast, but not especiallysensitive way of creating dotplots. It is an acceptable method fordisplaying regions of substantial similarity between two sequences. Using a longer word (tuple) size displays less random noise, runsextremely quickly, but is less sensitive. Shorter word sizes are moresensitive to shorter or fragmentary regions of similarity, but alsodisplay more random points of similarity (noise) and runs slower.
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