CloneSet3

Bio/SubsMat/MatrixInfo.py

Bio/SubsMat/MatrixInfo.py

# http://www.embl-heidelberg.de/~vogt/matrices/blosum50.cmp
blosum50 = {("W","F"):1,("L","R"):   -3,("S","P"):   -1,("V","T"):0,("Q","Q"):7,("N","A"):   -1,("Z","Y"):   -2,("W","R"):   -3,("Q","A"):   -1,("S","D"):0,("H","H"):10,("S","H"):   -1,("H","D"):   -1,("L","N"):   -4,("W","A"):   -3,("Y","M"):0,("G","R"):   -3,("Y","I"):   -1,("Y","E"):   -2,("B","Y"):   -3,("Y","A"):   -2,("V","D"):   -4,("B","S"):0,("Y","Y"):8,("G","N"):0,("E","C"):   -3,("Y","Q"):   -1,("Z","Z"):5,("V","A"):0,("C","C"):13,("M","R"):   -2,("V","E"):   -3,("T","N"):0,("P","P"):10,("V","I"):4,("V","S"):   -2,("Z","P"):   -1,("V","M"):1,("T","F"):   -2,("V","Q"):   -3,("K","K"):6,("P","D"):   -1,("I","H"):   -4,("I","D"):   -4,("T","R"):   -1,("P","L"):   -4,("K","G"):   -2,("M","N"):   -2,("P","H"):   -2,("F","Q"):   -4,("Z","G"):   -2,("X","L"):   -1,("T","M"):   -1,("Z","C"):   -3,("X","H"):   -1,("D","R"):   -2,("B","W"):   -5,("X","D"):   -1,("Z","K"):1,("F","A"):   -3,("Z","W"):   -2,("F","E"):   -3,("D","N"):2,("B","K"):0,("X","X"):   -1,("F","I"):0,("B","G"):   -1,("X","T"):0,("F","M"):0,("B","C"):   -3,("Z","I"):   -3,("Z","V"):   -3,("S","S"):5,("L","Q"):   -2,("W","E"):   -3,("Q","R"):1,("N","N"):7,("W","M"):   -1,("Q","C"):   -3,("W","I"):   -3,("S","C"):   -1,("L","A"):   -2,("S","G"):0,("L","E"):   -3,("W","Q"):   -1,("H","G"):   -2,("S","K"):0,("Q","N"):0,("N","R"):   -1,("H","C"):   -3,("Y","N"):   -2,("G","Q"):   -2,("Y","F"):4,("C","A"):   -1,("V","L"):1,("G","E"):   -3,("G","A"):0,("K","R"):3,("E","D"):2,("Y","R"):   -1,("M","Q"):0,("T","I"):   -1,("C","D"):   -4,("V","F"):   -1,("T","A"):0,("T","P"):   -1,("B","P"):   -2,("T","E"):   -1,("V","N"):   -3,("P","G"):   -2,("M","A"):   -1,("K","H"):0,("V","R"):   -3,("P","C"):   -4,("M","E"):   -2,("K","L"):   -3,("V","V"):5,("M","I"):2,("T","Q"):   -1,("I","G"):   -4,("P","K"):   -1,("M","M"):7,("K","D"):   -1,("I","C"):   -2,("Z","D"):1,("F","R"):   -3,("X","K"):   -1,("Q","D"):0,("X","G"):   -2,("Z","L"):   -3,("X","C"):   -2,("Z","H"):0,("B","L"):   -4,("B","H"):0,("F","F"):8,("X","W"):   -3,("B","D"):5,("D","A"):   -2,("S","L"):   -3,("X","S"):   -1,("F","N"):   -4,("S","R"):   -1,("W","D"):   -5,("V","Y"):   -1,("W","L"):   -2,("H","R"):0,("W","H"):   -3,("H","N"):1,("W","T"):   -3,("T","T"):5,("S","F"):   -3,("W","P"):   -4,("L","D"):   -4,("B","I"):   -4,("L","H"):   -3,("S","N"):1,("B","T"):0,("L","L"):5,("Y","K"):   -2,("E","Q"):2,("Y","G"):   -3,("Z","S"):0,("Y","C"):   -3,("G","D"):   -1,("B","V"):   -4,("E","A"):   -1,("Y","W"):2,("E","E"):6,("Y","S"):   -2,("C","N"):   -2,("V","C"):   -1,("T","H"):   -2,("P","R"):   -3,("V","G"):   -4,("T","L"):   -1,("V","K"):   -3,("K","Q"):2,("R","A"):   -2,("I","R"):   -4,("T","D"):   -1,("P","F"):   -4,("I","N"):   -3,("K","I"):   -3,("M","D"):   -4,("V","W"):   -3,("W","W"):15,("M","H"):   -1,("P","N"):   -2,("K","A"):   -1,("M","L"):3,("K","E"):1,("Z","E"):5,("X","N"):   -1,("Z","A"):   -1,("Z","M"):   -1,("X","F"):   -2,("K","C"):   -3,("B","Q"):0,("X","B"):   -1,("B","M"):   -3,("F","C"):   -2,("Z","Q"):4,("X","Z"):   -1,("F","G"):   -4,("B","E"):1,("X","V"):   -1,("F","K"):   -4,("B","A"):   -2,("X","R"):   -1,("D","D"):8,("W","G"):   -3,("Z","F"):   -4,("S","Q"):0,("W","C"):   -5,("W","K"):   -3,("H","Q"):1,("L","C"):   -2,("W","N"):   -4,("S","A"):1,("L","G"):   -4,("W","S"):   -4,("S","E"):   -1,("H","E"):0,("S","I"):   -3,("H","A"):   -2,("S","M"):   -2,("Y","L"):   -1,("Y","H"):2,("Y","D"):   -3,("E","R"):0,("X","P"):   -2,("G","G"):8,("G","C"):   -3,("E","N"):0,("Y","T"):   -2,("Y","P"):   -3,("T","K"):   -1,("A","A"):5,("P","Q"):   -1,("T","C"):   -1,("V","H"):   -4,("T","G"):   -2,("I","Q"):   -3,("Z","T"):   -1,("C","R"):   -4,("V","P"):   -3,("P","E"):   -1,("M","C"):   -2,("K","N"):0,("I","I"):5,("P","A"):   -1,("M","G"):   -3,("T","S"):2,("I","E"):   -4,("P","M"):   -3,("M","K"):   -2,("I","A"):   -1,("P","I"):   -3,("R","R"):7,("X","M"):   -1,("L","I"):2,("X","I"):   -1,("Z","B"):2,("X","E"):   -1,("Z","N"):0,("X","A"):   -1,("B","R"):   -1,("B","N"):4,("F","D"):   -5,("X","Y"):   -1,("Z","R"):0,("F","H"):   -1,("B","F"):   -4,("F","L"):1,("X","Q"):   -1,("B","B"):5} 

# http://www.embl-heidelberg.de/~vogt/matrices/blosum55.cmp
blosum55 = {("W","F"):1,("L","R"):   -3,("S","P"):   -1,("V","T"):0,("Q","Q"):7,("N","A"):   -1,("Z","Y"):   -2,("W","R"):   -3,("Q","A"):   -1,("S","D"):0,("H","H"):10,("S","H"):   -1,("H","D"):   -1,("L","N"):   -4,("W","A"):   -3,("Y","M"):0,("G","R"):   -3,("Y","I"):   -1,("Y","E"):   -2,("B","Y"):   -3,("Y","A"):   -2,("V","D"):   -4,("B","S"):0,("Y","Y"):8,("G","N"):0,("E","C"):   -3,("Y","Q"):   -1,("Z","Z"):5,("V","A"):0,("C","C"):13,("M","R"):   -2,("V","E"):   -3,("T","N"):0,("P","P"):10,("V","I"):4,("V","S"):   -2,("Z","P"):   -1,("V","M"):1,("T","F"):   -2,("V","Q"):   -3,("K","K"):6,("P","D"):   -1,("I","H"):   -4,("I","D"):   -4,("T","R"):   -1,("P","L"):   -4,("K","G"):   -2,("M","N"):   -2,("P","H"):   -2,("F","Q"):   -4,("Z","G"):   -2,("X","L"):   -1,("T","M"):   -1,("Z","C"):   -3,("X","H"):   -1,("D","R"):   -2,("B","W"):   -5,("X","D"):   -1,("Z","K"):1,("F","A"):   -3,("Z","W"):   -2,("F","E"):   -3,("D","N"):2,("B","K"):0,("X","X"):   -1,("F","I"):0,("B","G"):   -1,("X","T"):0,("F","M"):0,("B","C"):   -3,("Z","I"):   -3,("Z","V"):   -3,("S","S"):5,("L","Q"):   -2,("W","E"):   -3,("Q","R"):1,("N","N"):7,("W","M"):   -1,("Q","C"):   -3,("W","I"):   -3,("S","C"):   -1,("L","A"):   -2,("S","G"):0,("L","E"):   -3,("W","Q"):   -1,("H","G"):   -2,("S","K"):0,("Q","N"):0,("N","R"):   -1,("H","C"):   -3,("Y","N"):   -2,("G","Q"):   -2,("Y","F"):4,("C","A"):   -1,("V","L"):1,("G","E"):   -3,("G","A"):0,("K","R"):3,("E","D"):2,("Y","R"):   -1,("M","Q"):0,("T","I"):   -1,("C","D"):   -4,("V","F"):   -1,("T","A"):0,("T","P"):   -1,("B","P"):   -2,("T","E"):   -1,("V","N"):   -3,("P","G"):   -2,("M","A"):   -1,("K","H"):0,("V","R"):   -3,("P","C"):   -4,("M","E"):   -2,("K","L"):   -3,("V","V"):5,("M","I"):2,("T","Q"):   -1,("I","G"):   -4,("P","K"):   -1,("M","M"):7,("K","D"):   -1,("I","C"):   -2,("Z","D"):1,("F","R"):   -3,("X","K"):   -1,("Q","D"):0,("X","G"):   -2,("Z","L"):   -3,("X","C"):   -2,("Z","H"):0,("B","L"):   -4,("B","H"):0,("F","F"):8,("X","W"):   -3,("B","D"):5,("D","A"):   -2,("S","L"):   -3,("X","S"):   -1,("F","N"):   -4,("S","R"):   -1,("W","D"):   -5,("V","Y"):   -1,("W","L"):   -2,("H","R"):0,("W","H"):   -3,("H","N"):1,("W","T"):   -3,("T","T"):5,("S","F"):   -3,("W","P"):   -4,("L","D"):   -4,("B","I"):   -4,("L","H"):   -3,("S","N"):1,("B","T"):0,("L","L"):5,("Y","K"):   -2,("E","Q"):2,("Y","G"):   -3,("Z","S"):0,("Y","C"):   -3,("G","D"):   -1,("B","V"):   -4,("E","A"):   -1,("Y","W"):2,("E","E"):6,("Y","S"):   -2,("C","N"):   -2,("V","C"):   -1,("T","H"):   -2,("P","R"):   -3,("V","G"):   -4,("T","L"):   -1,("V","K"):   -3,("K","Q"):2,("R","A"):   -2,("I","R"):   -4,("T","D"):   -1,("P","F"):   -4,("I","N"):   -3,("K","I"):   -3,("M","D"):   -4,("V","W"):   -3,("W","W"):15,("M","H"):   -1,("P","N"):   -2,("K","A"):   -1,("M","L"):3,("K","E"):1,("Z","E"):5,("X","N"):   -1,("Z","A"):   -1,("Z","M"):   -1,("X","F"):   -2,("K","C"):   -3,("B","Q"):0,("X","B"):   -1,("B","M"):   -3,("F","C"):   -2,("Z","Q"):4,("X","Z"):   -1,("F","G"):   -4,("B","E"):1,("X","V"):   -1,("F","K"):   -4,("B","A"):   -2,("X","R"):   -1,("D","D"):8,("W","G"):   -3,("Z","F"):   -4,("S","Q"):0,("W","C"):   -5,("W","K"):   -3,("H","Q"):1,("L","C"):   -2,("W","N"):   -4,("S","A"):1,("L","G"):   -4,("W","S"):   -4,("S","E"):   -1,("H","E"):0,("S","I"):   -3,("H","A"):   -2,("S","M"):   -2,("Y","L"):   -1,("Y","H"):2,("Y","D"):   -3,("E","R"):0,("X","P"):   -2,("G","G"):8,("G","C"):   -3,("E","N"):0,("Y","T"):   -2,("Y","P"):   -3,("T","K"):   -1,("A","A"):5,("P","Q"):   -1,("T","C"):   -1,("V","H"):   -4,("T","G"):   -2,("I","Q"):   -3,("Z","T"):   -1,("C","R"):   -4,("V","P"):   -3,("P","E"):   -1,("M","C"):   -2,("K","N"):0,("I","I"):5,("P","A"):   -1,("M","G"):   -3,("T","S"):2,("I","E"):   -4,("P","M"):   -3,("M","K"):   -2,("I","A"):   -1,("P","I"):   -3,("R","R"):7,("X","M"):   -1,("L","I"):2,("X","I"):   -1,("Z","B"):2,("X","E"):   -1,("Z","N"):0,("X","A"):   -1,("B","R"):   -1,("B","N"):4,("F","D"):   -5,("X","Y"):   -1,("Z","R"):0,("F","H"):   -1,("B","F"):   -4,("F","L"):1,("X","Q"):   -1,("B","B"):5} 

 [[#variable61621d20]]= {("W","F"):1,("L","R"): -3,("S","P"): -1,("V","T"):0,("Q","Q"):7,("N","A"): -1,("Z","Y"): -2,("W","R"): -3,("Q","A"): -1,("S","D"):0,("H","H"):10,("S","H"): -1,("H","D"): -1,("L","N"): -4,("W","A"): -3,("Y","M"):0,("G","R"): -3,("Y","I"): -1,("Y","E"): -2,("B","Y"): -3,("Y","A"): -2,("V","D"): -4,("B","S"):0,("Y","Y"):8,("G","N"):0,("E","C"): -3,("Y","Q"): -1,("Z","Z"):5,("V","A"):0,("C","C"):13,("M","R"): -2,("V","E"): -3,("T","N"):0,("P","P"):10,("V","I"):4,("V","S"): -2,("Z","P"): -1,("V","M"):1,("T","F"): -2,("V","Q"): -3,("K","K"):6,("P","D"): -1,("I","H"): -4,("I","D"): -4,("T","R"): -1,("P","L"): -4,("K","G"): -2,("M","N"): -2,("P","H"): -2,("F","Q"): -4,("Z","G"): -2,("X","L"): -1,("T","M"): -1,("Z","C"): -3,("X","H"): -1,("D","R"): -2,("B","W"): -5,("X","D"): -1,("Z","K"):1,("F","A"): -3,("Z","W"): -2,("F","E"): -3,("D","N"):2,("B","K"):0,("X","X"): -1,("F","I"):0,("B","G"): -1,("X","T"):0,("F","M"):0,("B","C"): -3,("Z","I"): -3,("Z","V"): -3,("S","S"):5,("L","Q"): -2,("W","E"): -3,("Q","R"):1,("N","N"):7,("W","M"): -1,("Q","C"): -3,("W","I"): -3,("S","C"): -1,("L","A"): -2,("S","G"):0,("L","E"): -3,("W","Q"): -1,("H","G"): -2,("S","K"):0,("Q","N"):0,("N","R"): -1,("H","C"): -3,("Y","N"): -2,("G","Q"): -2,("Y","F"):4,("C","A"): -1,("V","L"):1,("G","E"): -3,("G","A"):0,("K","R"):3,("E","D"):2,("Y","R"): -1,("M","Q"):0,("T","I"): -1,("C","D"): -4,("V","F"): -1,("T","A"):0,("T","P"): -1,("B","P"): -2,("T","E"): -1,("V","N"): -3,("P","G"): -2,("M","A"): -1,("K","H"):0,("V","R"): -3,("P","C"): -4,("M","E"): -2,("K","L"): -3,("V","V"):5,("M","I"):2,("T","Q"): -1,("I","G"): -4,("P","K"): -1,("M","M"):7,("K","D"): -1,("I","C"): -2,("Z","D"):1,("F","R"): -3,("X","K"): -1,("Q","D"):0,("X","G"): -2,("Z","L"): -3,("X","C"): -2,("Z","H"):0,("B","L"): -4,("B","H"):0,("F","F"):8,("X","W"): -3,("B","D"):5,("D","A"): -2,("S","L"): -3,("X","S"): -1,("F","N"): -4,("S","R"): -1,("W","D"): -5,("V","Y"): -1,("W","L"): -2,("H","R"):0,("W","H"): -3,("H","N"):1,("W","T"): -3,("T","T"):5,("S","F"): -3,("W","P"): -4,("L","D"): -4,("B","I"): -4,("L","H"): -3,("S","N"):1,("B","T"):0,("L","L"):5,("Y","K"): -2,("E","Q"):2,("Y","G"): -3,("Z","S"):0,("Y","C"): -3,("G","D"): -1,("B","V"): -4,("E","A"): -1,("Y","W"):2,("E","E"):6,("Y","S"): -2,("C","N"): -2,("V","C"): -1,("T","H"): -2,("P","R"): -3,("V","G"): -4,("T","L"): -1,("V","K"): -3,("K","Q"):2,("R","A"): -2,("I","R"): -4,("T","D"): -1,("P","F"): -4,("I","N"): -3,("K","I"): -3,("M","D"): -4,("V","W"): -3,("W","W"):15,("M","H"): -1,("P","N"): -2,("K","A"): -1,("M","L"):3,("K","E"):1,("Z","E"):5,("X","N"): -1,("Z","A"): -1,("Z","M"): -1,("X","F"): -2,("K","C"): -3,("B","Q"):0,("X","B"): -1,("B","M"): -3,("F","C"): -2,("Z","Q"):4,("X","Z"): -1,("F","G"): -4,("B","E"):1,("X","V"): -1,("F","K"): -4,("B","A"): -2,("X","R"): -1,("D","D"):8,("W","G"): -3,("Z","F"): -4,("S","Q"):0,("W","C"): -5,("W","K"): -3,("H","Q"):1,("L","C"): -2,("W","N"): -4,("S","A"):1,("L","G"): -4,("W","S"): -4,("S","E"): -1,("H","E"):0,("S","I"): -3,("H","A"): -2,("S","M"): -2,("Y","L"): -1,("Y","H"):2,("Y","D"): -3,("E","R"):0,("X","P"): -2,("G","G"):8,("G","C"): -3,("E","N"):0,("Y","T"): -2,("Y","P"): -3,("T","K"): -1,("A","A"):5,("P","Q"): -1,("T","C"): -1,("V","H"): -4,("T","G"): -2,("I","Q"): -3,("Z","T"): -1,("C","R"): -4,("V","P"): -3,("P","E"): -1,("M","C"): -2,("K","N"):0,("I","I"):5,("P","A"): -1,("M","G"): -3,("T","S"):2,("I","E"): -4,("P","M"): -3,("M","K"): -2,("I","A"): -1,("P","I"): -3,("R","R"):7,("X","M"): -1,("L","I"):2,("X","I"): -1,("Z","B"):2,("X","E"): -1,("Z","N"):0,("X","A"): -1,("B","R"): -1,("B","N"):4,("F","D"): -5,("X","Y"): -1,("Z","R"):0,("F","H"): -1,("B","F"): -4,("F","L"):1,("X","Q"): -1,("B","B"):5} 
 

# http://www.embl-heidelberg.de/~vogt/matrices/blosum55.cmp
blosum55 

# http://www.embl-heidelberg.de/~vogt/matrices/blosum50.cmp
blosum50