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- Updated WWW: to a working link

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- 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)
This commit is contained in:
Greg Larkin 2011-04-22 18:59:11 +00:00
parent 3fcbbb8d24
commit 7a3687325a
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=273070
1 changed files with 17 additions and 14 deletions
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31
biology/dotter/pkg-descr
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@ -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