MDL test case: Chromo shadow family, Z=0.0

.

Partitioning defined by patterns:

~
  1. HuHP1_B MoMOD1_B MoMOD2_B PcHET1_B
  2. DmHP1_A DvHP1_A HuHP1_A MoMOD1_A
  3. MoMOD2_A PcHET1_A PcHET2_A MoCHD1_A
  4. MoMOD3 CeYO82 SmPAJ26 HuMG44
  5. DmPc Pf0131C CfTENV Ce29H12
  6. DmHP1_B DvHP1_B PcHET2_B SpSWI6_B
  7. CeT9A58 DmSuv39 MgGRH MgMAGGY
  8. SpSWI6_A FoSKPY ScYEZ4_A ScYEZ4_B
  9. CeYK9A3
  10. MoCHD1_B

Does this correspond to the tree?

We see that most of the groups correspond to dense subtrees in the tree, but not all the time. The groups are all of size 4 which was the minimum value used for K (minimum number of sequences to match a pattern for the pattern to be reported). When Z=0, the Pratt scoring is used directly, and the strongest patterns are ranked on top not depending on the number of sequences matching the pattern.

Patterns covering the set:

  1. HuHP1_B MoMOD1_B MoMOD2_B PcHET1_B 
    164.79366 164.79366 
I-I-G-A-T-D-x(0,1)-S-x(0,1)-G-[ED]-L-M-F-L-M-K-W-[KE]-x-[TS]-D-E-A-D-L-V-x-[AS]-x-[ED]-A-x(2)-K-C-P-Q-[ILV]-[IV]-I-x-F-Y-E-[KE]-[HR]-L-T-W
  2. DmHP1_A DvHP1_A HuHP1_A MoMOD1_A 
    159.42332 159.42332 
E-x(0,1)-E-x(0,1)-E-E-Y-x-V-E-K-[IV]-[IL]-D-R-R-V-x-K-G-x-V-E-Y-x-L-K-W-K-G-[FY]-x-[ED]-x-[HED]-N-T-W-E-P-E-x-N-L-D-C-x-[ED]-L-I
  3. MoMOD2_A PcHET1_A PcHET2_A MoCHD1_A 
    90.56201 90.56201 
E-x(3)-[IV]-x-[KR]-[IV]-x-D-x(0,1)-R-x(3,4)-G-x-[IV]-x-Y-x-[IL]-K-W-K-G-[FYW]-x-[HED]-x-[HED]-N-T-W-E-x(2)-E-[TN]-x-[KED]-x(3)-[LV]
  4. MoMOD3 CeYO82 SmPAJ26 HuMG44 
    73.45912 73.45912 
L-x(4)-[KR]-x(2)-[KER]-x-E-x(0,1)-Y-x(1,2)-K-W-x-G-[YW]-x(3)-[HED]-[SN]-[TS]-W-E-P-[KER]-x-N-[IL]-x(4)-[IL]-x(6)-[KDR]-x(3)-[KER]
  5. DmPc Pf0131C CfTENV Ce29H12 
    50.50769 50.50769 
Y-x(1,3)-V-K-W-x-G-[YW]-x(5)-T-W-E-P-[ER]-x-N-[IL]
  6. DmHP1_B DvHP1_B PcHET2_B SpSWI6_B 
    37.83844 37.83844 
L-x(8,9)-A-x(8,9)-N-x(3)-P-x(3)-[IL]-x-[FY]-Y-E-x-[HR]-L
  7. CeT9A58 DmSuv39 MgGRH MgMAGGY 
    30.93853 30.93853 
V-[KR]-W-x-G-Y-x(3,5)-T-x-E-x(8,9)-A
  8. SpSWI6_A FoSKPY ScYEZ4_A ScYEZ4_B 
    26.18215 26.18215 
L-[ILV]-K-W-x(8,9)-T-W-x(0,2)-E
  9. CeYK9A3 
    kwtgwshlhntwesenslalmnakglkkvqnyvkkqkevemwkr
  10. MoCHD1_B 
    ddlhkqyqiveriiahsnkqsaaglpdyyckwqglpysecswedgaliskkfqtcideyfsrnqskttpfk

Page compiled by: Inge Jonassen.

Chromo Test Set MDL.