Table 8 The HI rules learnt to identify 1CPC (C-Phycocyanin) are illustrated first in their original Prolog form and in English translation. Two sets of rules are shown those using HIall, and those learnt from HIseq. All numbers were discretised into 10 levels for ease of symbolic induction (1 low – 10 high).
From: Homology Induction: the use of machine learning to improve sequence similarity searches
| PDB 1CPC C-Phycocyanin | |
|---|---|
| HI all | |
| Prolog | |
| homologous(A) :- | |
| desc(A,chain), | |
| amino_acid_ratio_rule(A,h,1). | |
| homologous(A) :- | |
| keyword(A,phycobilisome). | |
| English | |
| A protein is homologous if | |
| a1 | it has the word 'chain' in its SWISS-PROT description line and |
| it has a level 1 histidine content in the residue chain and | |
| a2 | or it has the word 'phycobilisome' as a SWISS-PROT keyword. |
| HI seq | |
| Prolog | |
| homologous(A) :- | |
| amino_acid_ratio_rule(A,w,1), | |
| amino_acid_ratio_rule(A,h,1), | |
| amino_acid_pair_ratio_rule(A,l,r,10). | |
| homologous(A):- | |
| mol_wt_rule(A,3), | |
| sec_struc_distribution_rule(A,a,10). | |
| English | |
| A protein is homologous if | |
| s1 | it has a level 1 tryptophan content and |
| it has a level 1 histidine content and | |
| it has a level 10 leucine-arginine pair content. | |
| s2 | or |
| it has a level 3 molecular weight and | |
| it has a level 10 predicted α-helix content. | |