An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

Table 1 Alignment programs used for performance comparisons

program	version	command	structural?	reference
Foldalign	2.1.0	foldalign-global seq _filename	yes	[48]
LocARNA	0.99	mlocarna-p-sequ-local = 0 seq _filename	yes	[15]
Dynalign	*	cat opt_ file \| dynalign	yes	[13]
LaRA	1.3.1	lara-i seq_ filename	yes	[55]
StrAl	0.5.2	stral seq _filename	yes	[56]
MAFFT	6.240	ginsi seq _filename	no	[57]
ClustalW	1.83	clustalw seq_ filename-outfile = out_ filename	no	[58]

In this table, 'program' and 'version' columns indicate program names and their versions, respectively. In 'command' column, executable file names and options we used are listed. In 'structural?' column, 'yes' indicates structural RNA sequence alignment program, and 'no' represents non-structural sequence alignment program. RNAz 1.0 with a default setting was applied to the alignments provided by MAFFT and ClustalW. (*) Dynalign version 4.5 (with M = -99) was used for the alignment quality benchmark, and Dynalign version 4.3 (with M = 8) was used for the ncRNA prediction benchmark, where we used the values recommended by Dynalign for the other parameters except for the maximum number of structures = 1. The parameters and file names were written in opt_file and used to run Dynalign.

ISSN: 1471-2105