Direct Input Sequence Encoding

In the direct encoding, each molecular residue can be represented by its identity or its features. The most commonly used method for direct encoding involves the use of 

Encoding Method Residue/ Window Vector Size Vector or Scalar Value  

Vector of AA Alph. (BIN20) ANLAIDV 20x7 l,19x 0 llx0,1,8x0 9x0. 17x0,1,0,0  

PAM Substitution Vector ANLAIDV 20x7 Values varied 

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Input/Output sequence encoding methods (see Table 9.1) PRF direct encoding of residue profile a = a-helix fi = P-sheet C = random coil t = (5-reverse turn L = loop %AA = amino acid composition FEAT = indirect encoding of sequence features MF = memory factor dist = distance Map = Kohonen map (with dimensions). 

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