| IntaRNA |
| IntaRNA -t <input_file_query> -q <input_file_target> > <output_file> |
| RNAplex |
| RNAplfold -W <mirna_length> -u <mirna_length> -O --plex_output < <input_file> |
| RNAplex -l <mirna_length> -q <input_file_query> -t <input_file_target> -a ./ |
| RNAup |
| RNAup -w <mirna_length> -b -o -3 -5 --interaction_first < <input_file> |
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