[Blends-commit] r2861 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Mon Jun 27 12:57:23 2011
New Revision: 2861

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2861
Log:
Removed dotter because we have acedb-other-dotter

Modified:
    projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2861&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Mon Jun 27 12:57:23 2011
@@ -2159,36 +2159,6 @@
 Comment: BioLinux contains a dendroscope package which is available
  at http://www.dendroscope.org but this project has only a
  "free as in beer" binary download - so this is not for us ...
-
-Depends: dotter
-Homepage: http://sonnhammer.sbc.su.se/Dotter.html
-License: to be clarified
-Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
-Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Pkg-Description: detailed comparison of two sequences
- 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.
-Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
- .
- The package's homepage is currently unavailable but the source might be
- obtainable from freebsd.org.
 
 Depends: dotur
 Homepage: http://www.plantpath.wisc.edu/fac/joh/DOTUR/