High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH

Table 2 Comparison of the Compliance of Significance Scores with the SCOP Classification

Program	family	superfamily	fold
SABERTOOTH (struct)	96.85	91.54	90.29
SABERTOOTH (seq)	95.05	85.06	79.04
HHpred	94.84	89.55	75.69
PSI-BLAST B62	93.22	81.32	68.99
PSI-BLAST B80	92.53	81.88	69.74
PSI-BLAST B45	91.64	80.70	69.21
SABERTOOTH (seq/seqSim)	89.96	76.16	64.61
Clustal W	75.79	60.52	47.96
T-Coffee	68.01	52.87	47.65

The table shows the area under curve (AUC) in percentage for all programs and SCOP levels shown in Fig. 2, sorted by the first column. For 'SABERTOOTH (seq/seqSim)' significance is measured using the less accurate seqSim instead of the PSSM score, data is added for illustration. SABERTOOTH structure alignment is added for illustrative purposes, but it is not included in the comparison.

ISSN: 1471-2105