dotter 20021204 biology =0

BROKEN: checksum mismatch
IGNORE: is marked as broken: checksum mismatch
A viewer for multiple sequence alignments
Maintained by: fernan@iib.unsam.edu.ar
Port Added: 15 Mar 2006 10:36:50

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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
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://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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Required To Run: emulators/linux_base-fc4

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To install the port: cd /usr/ports/biology/dotter/ && make install clean

A package is not available for ports marked as: Forbidden / Broken / Ignore / Restricted

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Configuration Options

     No options to configure

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Master Sites:

http://sonnhammer.sbc.su.se/download/software/dotter/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/dotter-20021204/

- broken checksum mismatch

UNBREAK: Probably was a temporary failure, checksums are ok now.

Feature safe:   yes

- BROKEN checksum mismatch

- Fix fetch

PR:             137840
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

Umark BROKEN, stale distfile removed from ftp-master.

Mark BROKEN: does not fetch

Replace IGNORE with ONLY_FOR_ARCHS for this binary port.

Submitted by:   maintainer

Unmark BROKEN, it seems to be caused by a stale distfile on ftp-master.

Mark BROKEN: checksum mismatch

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>

5 vulnerabilities affecting 16 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities