Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)

Table 2 Detection performance of HMMs

Name	M	Organism	Chromosome	Threshold	Detected ( n)	Missed ( n)	Additional positive ( n)	Sensitivity (%)
Zam^a	290	Drosophila melanogaster	3L	23	6 (13)	4 (1)	80 (84)	60 (93)
Zam^a	290	Anopheles gambiae	2R	23	6 (13)	4 (1)	80 (84)	60 (93)
Mag C^b	50	Anopheles gambiae	2R	14	0 (0)	0 (12)	155	NA (0)
Mag A	90	Anopheles gambiae	2R	20	3 (25)	1 (34)	36	75 (42)
CsRN1	90	Anopheles gambiae	2R	12	1 (31)	0 (11)	117	100 (74)
Sushi	270	Danio rerio	7	35	8 (46)	24 (78)	122	25 (37)
rGmr1	150	Danio rerio	7	20	7 (35)	78 (260)	38	8 (12)
Sire	150	Oryza sativa	1	20	3 (10)	1 (3)	53	75 (77)
Retrofit	150	Oryza sativa	1	35	4 (8)	2 (2)	4	67 (80)

The detection performance was not extensively evaluated. The number of LTRs detected in one chromosome of a suitable eukaryotic organism, the number of LTRs missed and the number of additional positives as compared to the RepeatMasker output for the chosen chromosome are shown. The threshold, number of match states M and sensitivity are also tabulated. Two numbers for the sensitivity are reported, first the sensitivity for LTRs not belonging to the training set and second the sensitivity for all LTRs in the clade of interest between parentheses.
^aTwo chromosomes from different organisms were screened.
^bAll LTRs in the clade belonged to the training set.

ISSN: 1759-8753