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
biology/seqtools: Tools for visualising sequence alignments
Blixem is an interactive browser of pairwise alignments that have
been stacked up in a "master-slave" multiple alignment; it is not
a 'true' multiple alignment but a 'one-to-many' alignment.
Belvu is a multiple sequence alignment viewer and phylogenetic tool.
Dotter is a graphical dot-matrix program for detailed comparison
of two sequences.
WWW: http://www.sanger.ac.uk/resources/software/seqtools/
PR: ports/183801
Submitted by: Kurt Jaeger <fbsd-ports opsec.eu>
. give maintainership to the submitter;
. add one month to DEPRACATION_DATE;
while here: strip the indefinite article from COMMENT.
PR: ports/183742
Submitted by: Kurt Jaeger <fbsd-ports@opsec.eu> (assigned maintainer)
- 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)
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>
