PseAA

Dipeptide pseudo amino acid composition

The option of dipeptide composition will generate 420 components for each protein sequence, the first 20 components are the conventional amino acid composition(AAC); the following 400 components are the fractions of 400 dipeptides, i.e. AA, AC, AD,

, YV, YW, YY; the 400 components are calculated using the following equation,

where dep(i) is the i^th dipeptide of the 400 dipeptides, i=1,2,

,400.

The format of the output for the 420 components are:

1^st line: 20 components of amino acid composition (AAC);

2^nd line: 20 components of dipeptide composition beginning with amino acid A, i.e. AA, AC, AD,

, AY;

3^rd line: 20 components of dipeptide composition beginning with amino acid C, i.e. CA, CC, CD,

, CY;

21^st line: 20 components of dipeptide composition beginning with amino acid Y, i.e. YA, YC, YD,

, YY.

NOTE: in dipeptide pseudo amino acid composition, the other three parameters are NOT needed any more, i.e. amino acid attributes, normalization weight factor and lamda