20 lines
1.1 KiB
Text
20 lines
1.1 KiB
Text
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Dotter is a graphical dotplot program for detailed comparison of two sequences.
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Here, every residue in one sequence is compared to every residue in the other
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sequence. The first sequence runs along the x-axis and the second sequence
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along the y-axis. In regions where the two sequences are similar to each other,
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a row of high scores will run diagonally across the dot matrix. If you're
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comparing a sequence against itself to find internal repeats, you'll notice
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that the main diagonal scores maximally, since it's the 100% perfect
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self-match.
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To make the score matrix more intelligible, the pairwise scores are averaged
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over a sliding window which runs diagonally. The averaged score matrix forms a
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three-dimensional landscape, with the two sequences in two dimensions and the
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height of the peaks in the third. This landscape is projected onto two
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dimensions by aid of greyscales - the darker grey of a peak, the higher it is.
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Dotter provides a tool to explore the visual appearance of this landscape, as
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well as a tool to examine the sequence alignment it represents.
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WWW: http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html
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