Table 1.

Table of the RNA structural alignment algorithms under consideration for performance assessment in this study

Program	Package/Version	References
PARTS	RNAstructure 6.3	[17]
Dynalign2	RNAstructure 6.3	[15]
Foldalign	2.5.3	[37]
LocARNA	LocARNA 1.9.2	[21]
SPARSE	LocARNA 1.9.2	[22]
RNABERT	1.0.0	[28]
RNAmountAlign	1.0.0	[19]
LinearTurboFold	1.0.0	[23]

^†All algorithms were evaluated with default configurations, and the network model of RNABERT has been pretrained using the full Rfam 14.3 dataset [28]