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Table 1 Alignment programs used for performance comparisons

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

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]
  1. 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.