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Table 1 Features used for "soft" partitioning the input space (r denotes the length of the corresponding window)

From: A Hybrid Genetic-Neural System for Predicting Protein Secondary Structure

Feature Conjecture
1 Check whether hydrophobic aminoacids occur in the current window (r = 15) according to a clear periodicity (i.e., one every 3–4 residues) Alpha helices may sometimes fulfill this pattern
2 Check whether the current window (r = 13) contains numerous residues in {A,E,L,M} and few residues in {P,G,Y,S} Alpha helices are often evidenced by {A,E,L,M} residues, whereas {P,G,Y,S} residues account for their absence
3 Check whether the left side of the current window (r = 13) is mostly hydrophobic and the right part is mostly hydrophilic (and viceversa) Transmembrane alpha helices may fulfil this feature
4 Check whether, on the average, the current window (r = 11) is positively charged or not A positive charge might account for alpha helices or beta sheets
5 Check whether, on the average, the current window (r = 11) is negatively charged or not A negative charge might account for alpha helices or beta sheets
6 Check whether, on the average, the current window (r = 11) is neutral A neutral charge might account for coils
7 Check whether the current window (r = 11) mostly contains \small" residues Small residues might account for alpha helices or beta sheets
8 Check whether the current window (r = 11) mostly contains polar residues Polar residues might account for alpha helices or beta sheets