The directory T1-RNA-kinetic-simulation-scripts contain the kinetic simulation scripts for T1 RNA.

The directories T1-short, T1, T1-delAU, T1-add2bp, T2, T3, and T4 contain the filtering and the analytical scripts to obtain our desired RNA candidates (The Linux executable version of MC-Fold can be downloaded from https://www.major.iric.ca/MC-Fold/). The directory MCFOLD-DB is required when executing mcfold.static.exe.

Here are the candidate sequences we have selected for each RNA:

T1-short:
seq267: GGGAAGGGCAACUUUCA (T1-short)
seq608: GGGCCUUGCAAAGGGUA
(The full candidate list: T1-short/run_mcfold/set_all_Mcfold_2D_result_G_less_than_3/select_the_sample/step12_new_sort.out)

T1:
seq77:GGCGCGUACGGAAGGGCAACUUUCAUACCGCGCC
seq171:GGCGCGCCUGGAAGGGCAACUUUCACUUCGCGCC
seq1:GGCGCGAAAGGAAGGGCAACUUUCAAAACGCGCC (T1)
(The full candidate list: T1/run_mcfold/step_new_43_sort.out)

T1-delAU:
seq3:GGGAGGGCAACUUCA (T1-delAU)
(The full candidate list: T1-delAU/run_mcfold/step_new_43_sort.out)

T1-add2bp:
seq24:GGGGGAAGGGCAACUUUUCUA (T1-add2bp)
(The full candidate list: T1-add2bp/run_mcfold/step_new_43_sort.out)

T2:
seq89:GUUCCUGCAAAGGGAA (T2)
(The full candidate list: T2/run_mcfold/step_new_43_sort.out)

T3:
seq232: GGAGGUGGCAACGUCUA
seq297: GGGCAUGGCAAUGUGCA
seq320: GGGGAUGGCAAUGUCCA
seq256: GGGUAUGGCAAUGUACA (T3)
(The full candidate list: T3/run_mcfold/step_new_43_sort.out)

T4:
seq4:GGGAAGUGCGCGCUUCGGCGCGCCUUUCC (T4)
(The full candidate list: T4/run_mcfold/step_new_43_sort.out)