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comment	@# @;


1.2
date	2011.04.22.18.59.11;	author glarkin;	state Exp;
branches;
next	1.1;

1.1
date	2006.03.15.10.35.24;	author garga;	state Exp;
branches;
next	;


desc
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1.2
log
@- Updated WWW: to a working link
- 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)
@
text
@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.

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://sonnhammer.sbc.su.se/Dotter.html
@


1.1
log
@Add dotter 20021204 # last modified date in FTP server, a viewer for
multiple sequence alignments.

PR:		ports/93055
Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar>
@
text
@d1 7
a7 6
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
d11 6
a16 5
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.
d18 3
a20 2
Dotter provides a tool to explore the visual appearance of this landscape, as
well as a tool to examine the sequence alignment it represents.
d22 1
a22 1
WWW: http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html
@

