In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity

BMC Genomics

Table 4 Identified (miRNA) hairpins in genomes of C. elegans and four viruses

Organism	Identified miRNA hairpins ^a	Identified genomic hairpins	miRNA hairpins % (number) ^b			genomic hairpin loci % (number) ^b
			L = 1.0	L ≥ 0.05	L ≥ 1e-5	L = 1.0	L ≥ 0.05	L ≥ 1e-5
C. elegans	128/132	3,526,115	34 (45)	71 (94)	89 (117)	0.1 (3,110)	0.6 (21,313)	2.8 (98,309)
EBV	23/23	6,182	35 (8)	87 (20)	100 (23)	0.3 (20)	2.6 (162)	13 (793)
MDV	8/8	5,374	25 (2)	100 (8)	100 (8)	0.3 (15)	1.3 (69)	6.1 (329)
HCMV	10/11 ^c	9,747	40 (4)	90 (9)	100 (10)	0.3 (30)	2.5 (247)	12 (1,147)
KSHV	12/13 ^d	4,296	17 (2)	83 (10)	92 (11)	0.5 (20)	2.2 (94)	10 (433)

^a Identified miRNA hairpins/number of known miRNA hairpins in genome(s) in miRBase version 9.0 [44].
^b Percentage of miRNA or genomic hairpin loci that have at least a certain L-score for scoring model Metazoa (absolute numbers between brackets).
^c MiRNA hcmv-mir-UL148D could not be mapped on the genomic sequence of HCMV [EMBL: X17043].
^d MiRNA kshv-mir-K12-10b could not be mapped on the genomic sequence of KSHV [EMBL: U75698HCMV].

ISSN: 1471-2164