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authorGreg Larkin <glarkin@FreeBSD.org>2011-04-22 18:59:11 +0000
committerGreg Larkin <glarkin@FreeBSD.org>2011-04-22 18:59:11 +0000
commit7a3687325a2fba4b185b6853df3eedad3b884a64 (patch)
tree0c257fb2ad7d833210d94f05af343121686f51cb /biology
parent3fcbbb8d242de1463c80d07434827d671d6622a1 (diff)
downloadports-7a3687325a2fba4b185b6853df3eedad3b884a64.tar.gz
ports-7a3687325a2fba4b185b6853df3eedad3b884a64.zip
Notes
Diffstat (limited to 'biology')
-rw-r--r--biology/dotter/pkg-descr31
1 files changed, 17 insertions, 14 deletions
diff --git a/biology/dotter/pkg-descr b/biology/dotter/pkg-descr
index 1f04ae8b9118..e28a51ca02fe 100644
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+++ b/biology/dotter/pkg-descr
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-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