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

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