Fig. 7

Sensitivity of sequence search tools. a We searched with 6616 SCOP20 domain sequences through the UniProt plus SCOP20 database using one to three search iterations. The sensitivity to detect homologous sequences is measured by cumulative distribution of the Area Under the Curve 1 (AUC1), the fraction of true positives ranked better than the first false positive match. True positive matches are defined as being from the same SCOP superfamily [25], false positives have different SCOP folds, excepting known cases of inter-fold homologies. b Sensitivity of HHsearch with and without scoring secondary structure similarity, measured by the cumulative distribution of AUC1 for a comparison of 6616 profile HMMs built from SCOP20 domain sequences. Query HMMs include predicted secondary structure, target HMMs include actual secondary structure annotated by DSSP. True and false positives are defined as in A