MDL test case: Chromo shadow family, Z=4.0

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Partitioning defined by patterns:

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

Does this correspond to the tree?

The first set corresponds roughly to the set that Rein Aasland has called the ``classical chromo domains linked to chromo shadow domains'', and the second set corresponds to a relatively dense subtree/subset within what he calles ``chromo shadow domains''. The third and fourth are sets of sequences with no obvious relationship from the reported NJ tree. And the fifth and sixth are single sequences.

Patterns covering the set:

  1. DmHP1_A DvHP1_A HuHP1_A MoMOD1_A MoMOD2_A PcHET1_A PcHET2_A
    55.97691 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
    38.01233 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. DmPc MoMOD3 CeYO82 SmPAJ26 Pf0131C DmSuv39 HuMG44 CfTENV MoCHD1_A CeYK9A3 Ce29H12
    20.77766 32.65060 
    K-W-x-G-[YW]-x(5)-[TS]-W-E-x(3)-[TSN]-[ILV] 
    
  4. SpSWI6_A CeT9A58 ScYEZ4_A MoCHD1_B ScYEZ4_B MgGRH MgMAGGY PcHET2_B
    5.50508 11.01015 
    E-x(7,8)-L-x(0,2)-K 
    
  5. FoSKPY
    eisgpevyeaeairdtrkingqreylikwknypenentweppkhlvnaqrllkdfhqrarkkerrpk 
  6. SpSWI6_B
    vkqvenydswedlvssidtierkddgtleiyltwkngaishhpstitnkkcpqkmlqfyeshltfrene 
    

Page compiled by: Inge Jonassen.

Chromo Test Set MDL.