LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

Table 1 Benchmarking the performance of LTR_FINDER_parallel

Genome	Arabidopsis	Rice	Maize	Wheat
Version	TAIR10	MSU7	AGPv4	CS1.0
Size	119.7 Mb	374.5 Mb	2134.4 Mb	14,547.3 Mb
Original memory (1 thread^a)	0.37 Gbyte	0.55 Gbyte	5.00 Gbyte	11.88 Gbyte^b
Parallel memory (36 threads^a)	0.10 Gbyte	0.12 Gbyte	0.82 Gbyte	17.67 Gbyte
Original time (1 thread)	0.58 h	2.1 h	448.5 h	10,169.3 h^b
Parallel time (36 threads)	6.4 min	2.6 min	10.3 min	71.8 min
Speed up	5.4 X	48.5 X	2613 X	8498 X
# of LTR candidates (1 thread)	226	2851	60,165	231,043
# of LTR candidates (36 threads)	226	2834	59,658	237,352
% difference in candidate #	0.00%	0.60%	0.84%	−2.73%

^a Intel(R) Xeon(R) CPU E5–2660 v4 @ 2.00GHz
^b LTR_FINDER was run on each chromosome; the maximum memory and the total time are shown

ISSN: 1759-8753