Fig. 1

False-positive rates against median domain E-value cutoffs of the Pfam library (release 29) for HMMER2 and HMMER3 model builds. The HMMER2 (in solid red) and HMMER3 (in solid blue) plots are depicted with their IQRs (interquartile ranges) in dotted red and blue lines respectively. The average E-value cutoff of HMMER3 needs to be more stringent than HMMER2. The magnitude difference between them is about 10⁶ ~ 10¹¹. When one imposes the recommended E-value cutoff of 0.1 for HMMER2, the corresponding FPR will be at 5.60e-3 (see dotted vertical line) with 91 false-positives. The equivalent HMMER3 E-value will be 4.15e-7. For extreme stringency (i.e., FPR < 6.14e-5 or FP < 1), the required HMMER2 and HMMER3 E-value cutoffs are 2.13e-9 and at 1.35e-20 respectively (see leftmost dotted vertical line)