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DOTMATCHER application details page
Displays a thresholded 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(subject to threshold conditions) wherever there is a similarity betweenthe 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). dotmatcher uses a threshold to define whether a match is plotted(calculated from the substitution matrix). A window of specified lengthis moved up all possible diagonals and a score is calculated within eachwindow for each position along the diagonals. The score is the sum ofthe comparisons of the two sequences using the given similarity matrixalong the window. If the score is above the threshold, then a line isplotted on the image over the position of the window.
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