MDL test case: Chromo shadow family, Z=4.0, Z'=3..0

.

Gap penalty C=0.5

:
  1. DmHP1_A DvHP1_A HuHP1_A MoMOD1_A MoMOD2_A PcHET1_A PcHET2_A 
    55.54833 130.61278 
E-x(0,1)-E-E-[FY]-x-V-E-K-[IV]-[IL]-D-[KR]-R-x(3,4)-G-x-V-x-Y-x-L-K-W-K-G-[FY]-x-[ED]-x-[HED]-N-T-W-E-P-x(2)-N-x-[ED]-C-x-[ED]-L-[IL]
  2. DmHP1_B DvHP1_B HuHP1_B MoMOD1_B MoMOD2_B PcHET1_B 
    37.51233 114.03698 
L-x(2,3)-E-[KR]-I-[IL]-G-A-[TS]-D-[TSN]-x-G-[EDR]-L-x-F-L-x(2)-[FW]-[KE]-x(2)-D-x-A-[ED]-x-V-x-[AS]-x(2)-A-x(2)-K-x-P-x(2)-[IV]-I-x-F-Y-E
  3. MoMOD3 SmPAJ26 Pf0131C HuMG44 CfTENV MoCHD1_A Ce29H12 
    19.48789 46.47173 
Y-x(0,2)-L-x(0,1)-K-W-x-G-[YW]-x(3)-[HED]-x-[TS]-W-E-x-[ER]-x-[TN]-[IL]
  4. CeYO82 CeT9A58 DmSuv39 FoSKPY CeYK9A3 ScYEZ4_A MoCHD1_B ScYEZ4_B 
    10.39702 21.54403 
W-x(6)-[HE]-x-[TS]-W-E-x(4)-[ILV]

  5. DmPc SpSWI6_A MgGRH MgMAGGY PcHET2_B SpSWI6_B 
3.33672 11.51015 
G-x(7,8)-W-x(1,2)-G

Gap penalty C=1.0

:
  1. DmHP1_A DvHP1_A HuHP1_A MoMOD1_A MoMOD2_A PcHET1_A PcHET2_A 
    55.11976 129.61278 
E-x(0,1)-E-E-[FY]-x-V-E-K-[IV]-[IL]-D-[KR]-R-x(3,4)-G-x-V-x-Y-x-L-K-W-K-G-[FY]-x-[ED]-x-[HED]-N-T-W-E-P-x(2)-N-x-[ED]-C-x-[ED]-L-[IL]
  2. DmHP1_B DvHP1_B HuHP1_B MoMOD1_B MoMOD2_B PcHET1_B 
    37.34566 113.53698 
L-x(2,3)-E-[KR]-I-[IL]-G-A-[TS]-D-[TSN]-x-G-[EDR]-L-x-F-L-x(2)-[FW]-[KE]-x(2)-D-x-A-[ED]-x-V-x-[AS]-x(2)-A-x(2)-K-x-P-x(2)-[IV]-I-x-F-Y-E
  3. MoMOD3 SmPAJ26 Pf0131C HuMG44 CfTENV MoCHD1_A Ce29H12 
    18.84503 44.97173 
Y-x(0,2)-L-x(0,1)-K-W-x-G-[YW]-x(3)-[HED]-x-[TS]-W-E-x-[ER]-x-[TN]-[IL]
  4. CeYO82 CeT9A58 DmSuv39 FoSKPY CeYK9A3 ScYEZ4_A MoCHD1_B ScYEZ4_B 
    10.39702 21.54403 
W-x(6)-[HE]-x-[TS]-W-E-x(4)-[ILV]
  5. >DmPc SpSWI6_A MgGRH MgMAGGY PcHET2_B SpSWI6_B 
    3.00338 10.51015 
G-x(7,8)-W-x(1,2)-G

Note that the two different gap penalties give the same partition and the same patterns. The pattern scores are a bit different.

Page compiled by: Inge Jonassen.

Chromo Test Set MDL.