Table 2.

Initial number and types of different features used to encode sequence fragments

Feature types	Features	Number
Physicochemical property-based	Amino acid composition, average flexibility indices, hydrophobicity indices, net charge, partition coefficient, residue volume and molecular weight	147 (21 × 7)
Sequence-based	Binary-encoding	420 (21 × 20)
Structural level	Accessible surface area; secondary structure (coil, helix and strand) and disordered regions	105 (21 × 5)
Functional features	Gene ontology (GO) terms (1) biological process (BP), (2) molecular function (MF) and (3) cellular component (CC); protein domain and KEGG pathway	555 GO, 177 domain, 114 KEGG pathway
Functional annotation	UP_SEQ_FEATURE and UP_KEYWORDS	526