MDL test case: Chromo shadow family
.
For more information about this family see
Rein Aaslands Chromo Domain WWW page.
and
The chromo shadow domain,
a second chromo domain in Heterchromatinbinding protein 1, HP1.
Rein Aasland and A. Francis Stewart.
Nucleic Acids Research 23(16): 31683173 (1995)
Old results
Sequences included in the analysis:

Sequence segments included in Aasland and Stewart's NJ tree.

Bigger set.
NJ tree generated by using Clustal W(calculation) and Phylip (drawing).
The alignment that was used
to generate tree, made by Clustal W.
Aasland and Stewart's NJ tree showing an estimate of their evolutionary relationship:
New trees:
Results from running Pratt with the MDL set cover algorithm
First Pratt was run on the complete set of sequences, using different
Kvalues (minimum number of sequences to match a pattern). The pattern
having the maximum Cvalue was chosen, and the sequences matching this
pattern was removed from the set of sequences. The remaining set of
sequences were analysed in the same way. This was repeated until the
number of sequences left was less than 4. The resulting set of patterns
covers the set of sequences in a closetooptimal way according to the
Minimum Length Description (MDL) principle.
Different tests were done using different scoring schemes:

Using the equation given in the paper, C(p,l)=I(p)c0(c1 p + c2 #X(p) +c3)/l, and
parameters (c0,c1,c2,c3)=
(10,10,3,10).

Using the equation C(p,l)=I(p)(c1 p + c2 #X(p) +c3)/l (identical to the one
above except that c0 is not included). Different values for the parameters
were used; (c1,c2,c3)=

(8,3,50)

(8,3,100)

(8,3,150)

(8,3,300)

(3,2,50)

(10,2,50)

(10,2,100)

(12,2,100)

(15,2,50)
Example:
For the Z=5.0 example, we get sets of sizes: 7, 7, 12, and 8 (standard algorithm) and
7, 7, 11, 8, and 1 (complete). Examples of sequences of Kvalues used by the standard algorithm
when analysing sets of size N sequences:
Sequence of Kvalues used for N=34: 34, 29, 24, 20, 16, 13, 11, 9, 8, 7, 6, 5, 4.
Sequence of Kvalues used for N=27: 27, 24 20, 16, 13, 11, 9, 8, 7, 6, 5, 4.
Sequence of Kvalues used for N=18: 18, 16, 13, 11, 9, 8 7, 6, 5, 4.
Sequence of Kvalues used for N=13: 13, 11, 9, 8 7, 6, 5, 4.
We see that most of the chromo shadow domains are very seldom put
in the same group as any of the other sequences, and less often so than
some of the classical chromo domains liked to chromo shadow domains.
The chromo shadow domains also seem to constitute a more separate subtree than
the classical chromo domains liked to chromo shadow domains.
Page compiled by: Inge Jonassen.
MDL test cases,