. 2017 Apr 7;33(16):2487–2495. doi: 10.1093/bioinformatics/btx207

Table 1.

List of features used in the expression data analysis and their sources

Feature category	Features	Source software	Citations	Number of features
mRNA features	Codon composition (64 features)	Mfold, tAI	Markham and Zuker (2008) Chan and Lowe (2009)	81
	Nucleotide composition (4 features)
	Number and fraction of SD and SD-like sequences
	on forward and reverse strands (8 features)
	GC content of full sequence and first 30 nt
	RNA folding energy of full sequence and first 40 nt
	tRNA adaptation index
Amino acid properties	Amino acid composition (20 features)^a			29
Amino acid properties	% Aliphatic, Uncharged Polar, Polar, Hydrophobic, Positive, Negative, Sulfur- containing, Amide-containing and Alcohol- containing residues^a			29
PrEST physical properties	PrEST Length^a, Isoelectric Point^a, Molecular Weight^a	Biopython ProtParam	Cock et al. (2009) Gasteiger et al. (2003)	9
	Aromaticity and Instability^a
	Grand Average of Hydropathy (GRAVY)^a
	Absolute Charge and Charge per Residue^a
	Average Absolute Charge per Residue^a
Structural predictions	3-category Secondary Structures (3 features)	SCRATCH-1D	Cheng et al. (2005)	19
	8-category Secondary Structures (8 features)
	Solvent-accessible fraction
	Mean accessibility score
	GRAVY of outer and inner residues
	% Hydrophobic solvent-accessible residues
	% Hydrophobic solvent-inaccessible residues
	% Hydrophilic solvent-accessible residues
	% Hydrophilic solvent-inaccessible residues
Disorder predictions	Fraction of Disordered Residues as predicted by:	DisEBML DISOPRED3 RONN	Linding et al. (2003) Jones and Cozzetto (2015) Yang et al. (2005)	9
	−DisEMBL COILS, HOTLOOPS and REM 465
	−RONN and DISOPRED3
	Average Disorder Index (RONN and DISOPRED3)
	Protein-binding Fraction (DISOPRED3)
	Protein-binding Index (DISOPRED3)

Subset of features computed for solubility data