7a3687325a
- Copied unbranded distfile (dotter.LIN) to LOCAL/glarkin for mirroring to MASTER_SITE_LOCAL and prevention of fetch checksum error. [1] Reported by: pointyhat (via miwi)
22 lines
1.1 KiB
Text
22 lines
1.1 KiB
Text
Dotter is a graphical dotplot program for detailed comparison of
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two sequences. Here, every residue in one sequence is compared to
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every residue in the other sequence. The first sequence runs along
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the x-axis and the second sequence along the y-axis. In regions
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where the two sequences are similar to each other, a row of high
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scores will run diagonally across the dot matrix. If you're comparing
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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
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averaged over a sliding window which runs diagonally. The averaged
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score matrix forms a three-dimensional landscape, with the two
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sequences in two dimensions and the height of the peaks in the
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third. This landscape is projected onto two dimensions by aid of
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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
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landscape, as well as a tool to examine the sequence alignment it
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represents.
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WWW: http://sonnhammer.sbc.su.se/Dotter.html
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