dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity

Table 1 Classification of sequence-to-domain alignment HMMER2 and HMMER3 hits

Version	Classification	Original E-value	Fold-critical E-value	Remnant E-value
HMMER2	TP (True-positive)	≤0.1	≤10^−3.45	-
	FP (False-positive)	≤0.1	>10^−3.45	≤10^−3.45
	TN (True-negative)	>0.1	>10^−3.45	-
	FN (False-negative)	>0.1	≤10^−3.45	-
HMMER3	TP (True-positive)	≤10⁻³	≤10⁻⁶	-
	FP (False-positive)	≤10⁻³	>10⁻⁶	≤10⁻⁶
	TN (True-negative)	>10⁻³	>10⁻⁶	-
	FN (False-negative)	>10⁻³	≤10⁻⁶	-

The original E-value of hit is set at 0.1 as recommended by the HMMER2 manual [32] which gives a false-positive rate of 0.53. Using the latter as reference, the equivalent original E-value for HMMER3 is set at 10⁻³ (false-positive rate of 0.55). For the fold-critical E-value, the false-positive rate is preset at 0.1. These corresponds to the values of 10^–3.45 and 10^–6, respectively. ‘-’ denotes “don’t care” condition

ISSN: 1745-6150