Table 1. Software for feature prediction.

Feature Group	Program	Reference
Amino acid composition	in-house C++ code	NA
Sequence features	in-house C++ code	NA
Transmembrane segments	MEMSAT-SVM	[27]
Secondary structure	PSIPRED 3.3	[28]
Intrinsically disordered regions	DISOPRED 2.43	[29]
Signal peptides	SignalP 4.0	[16]
Subcellular localization	WoLF PSORT 0.2	[15]
PEST regions	epestfind in EMBOSS 6.4.0	[30]
Low complexity regions	Pfilt	[31]
Coiled coils	COILS 2.2	[32]
Phosphorylation sites	NetPhos 3.1	[33]
N-linked glycosylation sites	NetNGlyc 1.0c	[33]
O-GalNAc-glycosylation sites	NetOGlyc 3.1d	[34]

For any input amino acid sequence, FFPred 2.0 calculates several feature groups that are listed in the first column. The second and third columns report the name of the package used and the relevant literature citation respectively.