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Table 5 Sequential Predicates

From: A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models

Property/amino acid set Predicate
1- small {A,G,S,T} small(X,Y)
2- polar {D,E,H,K,N,Q,R,S,T,W,Y} polar(X,Y)
3- polar uncharged {N,Q} polarUncharged(X,Y)
4- aromatic {F,H,W,Y} aromatic(X,Y)
5- charged {D,E,H,I,K,L,R,V} charged(X,Y)
6- positively charged {H,K,R} positivelyCharged(X,Y)
7- negatively charged {D,E} negativelyCharged(X,Y)
8- tiny {A,G} tiny(X,Y)
9- bulky {F,H,R,W,Y} bulky(X,Y)
10- aliphatic {I,L,V} aliphatic(X,Y)
11- hydrophobic {I,L,M,V} hydrophobic(X,Y)
12- hydrophilic basic {K,R,H} hydrophilicBasic(X,Y)
13- hydrophilic acidic {E,D,N,Q} hydrophilicAcidic(X,Y)
14- neutral weakly hydrophobic {A,G,P,S,T} neutralWeakHydrophobic(X,Y)
15- hydrophobic aromatic {F,W,Y} hydrophobicAromatic(X,Y)
16- acidic {E,D} acidic(X,Y)
17- amino acid ratio aminoacidRatio(X,W,Y)
18- amino acid pair ratio aminoacidPairRatio(X,W,Y)
  1. For each predicate like property(X, Y) numbered from 1 to 18, X is the sequence identifier, Y is the percentage of amino acids with some physico-chemical property. For the predicate aminoacidRatio(X, W, Y), X is the sequence identifier, W is an amino acid, and Y is the percentage of amino acid W within sequence X. For the predicate aminoacidPairRatio(X, W, Y), X and Y are defined as before, and W is a pair of amino acids.