Table 2.

Protein features used in SecretomeP and the programs it utilizes internally to calculate them.

Protein feature	Dependency	Reference
Number of atoms	-	-
Number of positively charged residues	-	-
Low-complexity regions	SEG	Wootton and Federhen, 1996
Sub-cellular localisation	PSORT II	Nakai and Horton, 1999
Transmembrane helices	TMHMM 2.0c	Krogh et al., 2001
Pro-peptide prediction	ProP 1.0c	Duckert et al., 2004

- indicates feature calculated internally without any external dependency.