diff options
author | Greg Larkin <glarkin@FreeBSD.org> | 2011-04-22 18:59:11 +0000 |
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committer | Greg Larkin <glarkin@FreeBSD.org> | 2011-04-22 18:59:11 +0000 |
commit | 7a3687325a2fba4b185b6853df3eedad3b884a64 (patch) | |
tree | 0c257fb2ad7d833210d94f05af343121686f51cb /biology | |
parent | 3fcbbb8d242de1463c80d07434827d671d6622a1 (diff) |
Notes
Diffstat (limited to 'biology')
-rw-r--r-- | biology/dotter/pkg-descr | 31 |
1 files changed, 17 insertions, 14 deletions
diff --git a/biology/dotter/pkg-descr b/biology/dotter/pkg-descr index 1f04ae8b9118..e28a51ca02fe 100644 --- a/biology/dotter/pkg-descr +++ b/biology/dotter/pkg-descr @@ -1,19 +1,22 @@ -Dotter is a graphical dotplot program for detailed comparison of two sequences. -Here, every residue in one sequence is compared to every residue in the other -sequence. The first sequence runs along the x-axis and the second sequence -along the y-axis. In regions where the two sequences are similar to each other, -a row of high scores will run diagonally across the dot matrix. If you're -comparing a sequence against itself to find internal repeats, you'll notice +Dotter is a graphical dotplot program for detailed comparison of +two sequences. Here, every residue in one sequence is compared to +every residue in the other sequence. The first sequence runs along +the x-axis and the second sequence along the y-axis. In regions +where the two sequences are similar to each other, a row of high +scores will run diagonally across the dot matrix. If you're comparing +a sequence against itself to find internal repeats, you'll notice that the main diagonal scores maximally, since it's the 100% perfect self-match. -To make the score matrix more intelligible, the pairwise scores are averaged -over a sliding window which runs diagonally. The averaged score matrix forms a -three-dimensional landscape, with the two sequences in two dimensions and the -height of the peaks in the third. This landscape is projected onto two -dimensions by aid of greyscales - the darker grey of a peak, the higher it is. +To make the score matrix more intelligible, the pairwise scores are +averaged over a sliding window which runs diagonally. The averaged +score matrix forms a three-dimensional landscape, with the two +sequences in two dimensions and the height of the peaks in the +third. This landscape is projected onto two dimensions by aid of +greyscales - the darker grey of a peak, the higher it is. -Dotter provides a tool to explore the visual appearance of this landscape, as -well as a tool to examine the sequence alignment it represents. +Dotter provides a tool to explore the visual appearance of this +landscape, as well as a tool to examine the sequence alignment it +represents. -WWW: http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html +WWW: http://sonnhammer.sbc.su.se/Dotter.html |