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Fig. 6 | Biology Direct

Fig. 6

From: xHMMER3x2: Utilizing HMMER3’s speed and HMMER2’s sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

Fig. 6

HMMER2/HMMER3 E-value (in log10 scale) plot and false-positive difference histogram of the UniProt/SwissProt human sequence domain hits. a depicts 23622 pairs of HMMER2/HMMER3 E-values where the blue points denotes cases where the estimated FP values of the pair matched, while the red points denote the unmatched cases. About 86.5% of the pairs show higher stringency of HMMER2 E-values over HMMER3, and vice versa for the remaining pairs. b shows the histogram of the 23622 pairs of FP difference (i.e., FPH2-FPH3) values of the paired HMMER2/HMMER3 hits. Basically, 95% of the data points converge to the singular point at FPH2 = FPH3 or 0 (see blue dot). If small estimates of FPH2-FPH3 = ±4 (see vertical dotted lines) are included, the overall concordance of the HMMER pairs is about 98% of the data points. - The left skewness implies that a handful 389 data pairs exhibits higher HMMER3 FPR than that of HMMER2. These pairs are highlighted for annotation inconsistency as a result of FPR quantification by xHMMER3x2

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