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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 < Cfam_210557.fa

>Cfam_210557
AAAGGAUCCUCAUUAAGGUGGGUGGAAUAGUAUAACAAUAUGCUAAAUGUUGUUAUAGUAUCCCACCUACCCUGAUGUAUCUUUA
.((((((...(((((.(((((((((.(((.(((((((((((.....))))))))))).))).))))))))).))))).)))))). (-39.60)
.((((((...(((((.(((((((((.(((.(((((((((((.....))))))))))).))).))))))))).))))).)))))). [-39.84]
.((((((...(((((.(((((((((.(((.(((((((((((.....))))))))))).))).))))))))).))))).)))))). {-39.60 d=0.60}
 frequency of mfe structure in ensemble 0.671998; ensemble diversity 1.12  


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

Cfam_210557 secondary structure

Pair probabilities of base pairs in MFE structure

Cfam_210557 pair probabilities

01
pair probabilities

Positional entropy of base pairs in MFE structure

Cfam_210557 positional entropy

00.6
positional entropy