Table 1.

Accuracy of SISSIz and RNAz on RFAM sub-alignments

Alignment source	Algorithm	Sensitivitya	Specificitya,b
			SISSIz-s	Multiperm
Native RFAM	RNAz	17.7	99.8	100
	SISSIz	37.8	99.0	92.3
	SISSIz + RIBOSUM	40.9	99.2	90.8
Emulated genomicc	RNAz	16.1	99.7	99.8
	SISSIz	30.3	99.0	93.2
	SISSIz + RIBOSUM	34.3	99.6	93.0

^aUsing a confidence threshold half way between those reported in Figure 1 (Z-score ≤ −3 for SISSIz; P ≥ 0.75 for RNAz).

^bFrom the associated dinucleotide-controlled shuffled alignments.

^cSelected RFAM sequences are de-gapped and realigned with MAFFT-GINSI (42). RNAz predictions for alignments >300 nt were not calculated.

Values reflect the cumulative specificity for 10 200 and 6800 alignments of 10, 20 and 30 sequences with window lengths of 100, 200, 300 for SISSIz; 100 and 200 for RNAz, respectively. RNAz scoring for native RFAM alignments used the ‘−l’ option for structure alignments.