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miROrtho: the catalogue of animal microRNA genes


Some basic information about the miRNA precursor

  • The output of RNAfold including the:
    • minimum free folding energy structure with energy
    • thermodynamic ensemble structure with energy
    • centroid structure with ensemble distance
  • Secondary structure with the mature miRNA in red
  • Secondary structure color-coded according to pair probabilities of the MFE in the structure ensemble
  • Secondary structure color-coded according to positional entropy of the MFE in the structure ensemble
The color-coded secondary structures allow an estimation of the stability/reliability of the structure itself. Briefly high values (red) close to 1 for the pair probabilities are better as the pairs are highly frequent in the structure ensemble. Controversially for the positional entropy lower values close to 0 (red) are better as this represents less structural variability for one specific position. In other word, the structure is well defined and dominates the ensemble of structures.
Command line: RNAfold -d2 -noLP -p2 < Drer_210436.fa

>Drer_210436
CACCCAAGGGAUCUGCUUUAAGGUGGGUGGAGUAGUAUAACAAUAUGGCCCAUGUUGUUAUAGUAUCCCACCUACCCUGAUGUAGGCCGGGGGU
.((((...((.(((((.(((.(((((((((..((.((((((((((((...)))))))))))).))..))))))))).))).)))))))..)))) (-48.10)
.((((..,({.(((((.(((.(((((((((.,((.((((((((((((...)))))))))))).)),.))))))))).))).)))))))..)))) [-49.35]
.((((...((.(((((.(((.(((((((((..((.((((((((((((...)))))))))))).))..))))))))).))).)))))))..)))) {-48.10 d=4.05}
 frequency of mfe structure in ensemble 0.131788; ensemble diversity 5.65  


Secondary structure: Mature region(s) are marked in red

Drer_210436 secondary structure

Pair probabilities of base pairs in MFE structure

Drer_210436 pair probabilities

01
pair probabilities

Positional entropy of base pairs in MFE structure

Drer_210436 positional entropy

01.1
positional entropy
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