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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 < Trub_210529.fa

>Trub_210529
AAAAGGAUCCCCAUUAAGGUGGGUGGAAUAGUAUAACAAUGUGUCCAAUGUUGUUAUAGUAUCCCACCUACCCUGAUGUAGCUUUGC
..((((.....(((((.(((((((((.(((.(((((((((((.....))))))))))).))).))))))))).)))))...)))).. (-35.60)
..((((.....(((((.(((((((((.(((.(((((((({{(.....)}})))))))).))).))))))))).)))))...)))).. [-36.25]
..((((.....(((((.(((((((((.(((.(((((((((((.....))))))))))).))).))))))))).)))))...)))).. {-35.60 d=2.67}
 frequency of mfe structure in ensemble 0.34909; ensemble diversity 3.98  


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

Trub_210529 secondary structure

Pair probabilities of base pairs in MFE structure

Trub_210529 pair probabilities

01
pair probabilities

Positional entropy of base pairs in MFE structure

Trub_210529 positional entropy

01.4
positional entropy