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We will assume
that all these setup operations have been
successfully
completed. Note that the methods described below are
valid for both
DNA
and
protein
sequences.
compare calculates the dots to be displayed later , comes
with two different
algorithms; the "window/stringency" as default.
You might try
compare -word
for really large sequences.
dotplot displays dots calculated by compare, and will look
nicer if you
use additional options like the following.
For an overview of possible options, use dotplot
with the "check" option.
Recommendation for the 'dotplot' program:
Nicer figures will be obtained if you give the following
command line options.
If
you use
WPI,
make sure that the command line options
are ticked as indicated
below.
dotplot -tickaxes -symbol=2 -font=3
================================= Begin Exercise 8
Schematic pairwise DNA analysis:
Compare two sequences using the 'dotplot' technique.
Using previous exercise results, you should have
two DNA sequences
by now:
my1.seq
as the typed-in sequence, and
my2.seq
as the reading-frame extracted DNA sequence from the
seqed
exercise.
You shall compare these two sequences now.
To solve this problem, follow this schedule:
================================= End Exercise 8
It is important to know as much about the sequence
of interest
as possible. The
dotplot
as explained above may be used to analyse
sequences
internally,
i.e., you may compare a sequence against itself. The dotplot
as such becomes perfectly symmetrical.
The gcg implementation
of the 'dotplot' program will recognise that the sequences on both axes
are identical
and will, therefore, plot only half of the sequence. You might want to
force
a full display with
% dotplot -all
The benefit of an internal repeat analysis will be obvious if you
encounter
gene
duplication
or the occurrence of several functional protein motifs.
================================= Begin Exercise 9
Using previous exercise
results, you should have a database DNA sequence
my2.seq,
and the translated
sequence,
m19311.pep
as peptide.
You shall compare these two sequences now
with itself on each
DNA and protein level, and compare the results. Note that, in particular
on protein level, the adjustment of window and stringency values might
be a lengthy process.
To solve this problem, follow this schedule:
Tip for the Superimposition of Dotplots:
All gcg graphics routines offer a "density" to plot the output.
If you do not accept the default value but use a number dividable
by three for DNA, and the
corresponding number for the protein
comparison.
================================= End Exercise 9
Subsection 9.2.1 Comparison Calculation
Subsection 9.2.2 Display Program
Subsection 9.2.3 Detection of Internal Repeats
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