ProGeRF: Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function
Table 1
Comparison of amount detection and execution times (in seconds) of Mreps, Misa, Sputnik, GMATo, SciRoKo, TRF, and ProGeRF. The features were run on a Dell Inspiron, Intel core 2 duo 2.2 GHz processor with 2 MB cache, 3 GB RAM, 320 GB hard drive, Ubuntu operating system 14.04 LTS 32 bits.
Sequence
Mreps
Misa
Sputnik
GMATo
SciRoKo
TRF
ProGeRF
Rep (time)
Rep (time)
Rep (time)
Rep (time)
Rep (time)
Rep (time)
Rep (time)
NC_004318.1 (1204 kb)
9608 (2.8)
22867 (3.2)
7420 (0.7)
23539 (10.3)
3763 (1.1)
30244 (72.4)
26164 (3.9)
NC_001136.8 (1531 kb)
935 (1.4)
10640 (3.3)
1427 (0.9)
10721 (7.7)
185 (0.7)
8101 (4.5)
11552 (2.4)
NC_000962.2 (4411 kb)
1412 (3.9)
6832 (8.9)
3140 (1.46)
6846 (12.1)
72 (1.5)
19496 (24.5)
11422 (4.0)
Setaria* (15 Mb)
— (—)
2054241 (868.3)
480644 (105.7)
2073643 (9859.1)
47770 (129.0)
2438036 (1481.5)
2319812 (1352.0)
Whole genome. The value in brackets is the runtimes in seconds.
