TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins

BMC Bioinformatics

Table 3 Ability of program to differentiate between various protein classes.

*A. Plain*	% Sensitivity	% Specificity	% PPV	% NPV	% Accuracy
*bbtm vs ntm*	83	87	86.5	83.7	85
bbtm vs ahtm	83	72	74.8	80.1	77.5
*B. Evolutionary Information plus weighted AAs*	% Sensitivity	% Specificity	% PPV	%NPV	% Accuracy
bbtm vs ntm	91	94	93.8	91.3	92.5
bbtm vs ahtm	88	97	96.7	88.9	92.5

A shows the ability of the program to differentiate between various protein classes without inclusion of evolutionary information or differential amino acid weightings. B shows the improvements given the inclusion of these features. Performance was assessed using the 'leave homologues out' cross-validation.

ISSN: 1471-2105