A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures

BMC Bioinformatics

Table 5 Comparison of Iterative HFold F-measure with ShapeKnots on SHAPE data

Training set	Len	PK	Iter. HFold			ShapeKnots
			sen	ppv	F	sen	ppv	F
Pre-Q1 riboswitch, B. subtilis	34	1	62.5	100	76.9	100	100	100
Telomerase pseudoknot, human	47	1	100	100	100	100	100	100
tRNA(asp), yeast	75	0	81.0	100	89.5	95.2	95.2	95.2
TPP riboswitch, E. coli	79	0	46.5	47.6	47.1	95.4	87.5	91.3
SARS corona virus pseudoknot	82	1	69.2	86.3	69.2	84.6	88.0	86.3
cyclic-di-GMP riboswitch, V. cholerae	97	0	85.5	81.0	83.2	89.3	86.2	87.7
SAM I riboswitch, T. tengcongenis	118	1	79.5	91.2	84.9	92.3	97.3	94.7
M-Box riboswitch, B. subtilis	154	0	87.5	91.3	89.4	87.5	91.3	89.3
P546 domain, bI3 group I intron	155	0	55.4	57.4	56.4	94.6	96.4	95.5
Lysine riboswitch, T. maritima	174	1	85.7	94.7	90.0	87.3	88.7	88.0
Group I intron, Azoarcus sp.	214	1	52.4	54.1	53.2	92.1	95.1	93.5
Signal recognition particle RNA, human	301	0	70.0	73.7	71.8	55.0	53.9	54.4
Hepatitis C virus IRES domain	336	1	71.2	74.0	72.5	92.3	96.0	94.1
RNase P, B. subtilis	405	1	55.7	59.3	57.4	75.6	79.8	77.7
Group II intron, O. iheyensis	412	1	87.9	95.9	91.7	93.2	97.6	95.3
Group I intron, T. thermophila	425	1	83.2	85.2	84.2	93.9	91.2	92.5
5’ domain of 23S rRNA, E. coli	511	0	84.0	72.5	77.8	92.4	76.4	83.6
5’ domain of 16S rRNA, E. coli	530	0	73.6	69.0	71.2	89.9	80.6	84.9
Test set	Len	PK	Iter. HFold			ShapeKnots
			sen	ppv	F	sen	ppv	F
Fluoride riboswitch, P. syringae	66	1	100	100	100	93.7	93.7	93.7
Adenine riboswitch, V. vulnificus	71	0	100	100	100	100	100	100
tRNA(phe), E. coli	76	0	100	100	100	100	84.0	91.3
5S rRNA, E. coli	120	0	91.4	91.4	91.4	85.7	76.9	81.1
5’ domain of 16S rRNA, H. volcanii	473	0	90.3	82.3	86.1	89.6	82.7	86.0
HIV-1 5’ pseudoknot domain	500	1	45.4	50.4	47.7	100	100	100

ISSN: 1471-2105