ProGeRF: Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function
Table 2
Loci and nucleotide coverage between tools.
Sequence
B
Tools
Mreps
Misa
Sputnik
GMATo
SciRoKo
TRF
ProGeRF
Plasmodium Chr4 NC_004318.1
A
Mreps
—
78 (45)
53 (33)
78 (45)
41 (36)
98 (74)
89 (60)
Misa
47 (63)
—
21 (4)
100 (99)
18 (40)
88 (79)
100 (98)
Sputnik
91 (86)
70 (74)
—
70 (74)
58 (69)
0 (0)
83 (84)
GMATo
49 (62)
100 (99)
21 (40)
—
19 (40)
89 (79)
100 (98)
SciRoKo
96 (95)
93 (76)
95 (71)
92 (76)
—
95 (96)
98 (91)
TRF
51 (41)
54 (32)
0 (0)
54 (32)
16 (21)
—
68 (46)
ProGeRF
46 (56)
86 (67)
21 (31)
86 (67)
16 (32)
87 (78)
—
SAC Chr4 NC_001136.8
A
Mreps
—
60 (40)
42 (26)
68 (40)
18 (20)
95 (74)
86 (62)
Misa
7 (12)
—
3 (7)
100 (99)
1 (4)
33 (37)
100 (99)
Sputnik
30 (35)
29 (30)
—
29 (30)
12 (1)
74 (73)
38 (39)
GMATo
7 (12)
100 (99)
3 (7)
—
1 (4)
33 (37)
100 (99)
SciRoKo
91 (89)
77 (61)
86 (59)
77 (61)
—
99 (99)
94 (72)
TRF
15 (16)
41 (26)
13 (12)
41 (26)
2 (5)
—
48 (35)
ProGeRF
8 (16)
92 (80)
4 (7)
92 (80)
1 (5)
34 (39)
—
MTB H37Rv NC_000962.2
A
Mreps
—
9 (3)
15 (7)
9 (3)
3 (3)
91 (71)
75 (58)
Misa
2 (3)
—
1 (1)
100 (99)
0.5 (1)
13 (13)
100 (99)
Sputnik
6 (7)
2 (2)
—
2 (2)
1 (1)
66 (64)
14 (14)
GMATo
2 (3)
100 (99)
1 (1)
—
0.5 (1)
13 (13)
100 (99)
SciRoKo
73 (74)
47 (36)
63 (41)
47 (36)
—
100 (100)
79 (72)
TRF
8 (7)
4 (1)
10 (7)
4 (1)
0.4 (0.5)
—
18 (13)
ProGeRF
9 (16)
60 (35)
4 (4)
60 (35)
0.5 (1)
29 (33)
—
Percentage of the total number of detections (perfect and imperfect) of tools A also detected (i.e., covered) by tools B. The value in brackets is the proportion of nucleotides detected by A and covered by B.
