Table 2.

Performance comparison of LIR identification in NT_022853 with different tools

Parameter	Lirex	IRF	EMBOSS palindrome	detectIR	MATLAB palindrome
Setting	Window size: 2000 bp Minimum length: 30 bp Seed size: 5 bp	T4 class Maximum search distance: 74 bp T5 class Maximum search distance: 493 bp T7 class Maximum search distance: 10,000 bp Maximum loop: 2000 bp Maximum stem: 10,000 bp	For perfect LIRs minpallen: 30 bp maxpallen: 1000 bp gaplimit: 0 For imperfect LIRs minpallen: 30 bp maxpallen: 1000 bp gaplimit: 2 bp	For perfect LIRs minLen: 60 bp maxLen: 2000 bp For imperfect LIRs minLen: 60 bp maxLen: 2000 bp maxMismcNum: 6 bp	For perfect LIRs Length: 60 bp For imperfect LIRs Length: 60 bp Gap: 2 bp
Running time	∼9 h	1 min	14.2 min + 39.2 min	1.5 s + 13 s	2.9 s + 7.2 s
Number of perfect LIRs	28	7	8	19	7
Number of imperfect LIRs	1415	198	419	324	8
Total	1443	205	427	343	15

Note: The complete sequence of NT_022853.16 was examined for identification of LIRs using different tools. For detectIR and MATLAB palindrome, length refers to the sum of both stem size and loop size. LIR, long inverted repeat.