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 < Xtro_210532.fa

....(((....(((((.(((((((((.(((.(((((((((((.....))))))))))).))).))))))))).))))).....))). (-35.40)
....(((....(((((.(((((((((.(((.(((((((({{(.....)}})))))))).))).))))))))).))))).....))). [-35.98]
....(((....(((((.(((((((((.(((.(((((((((((.....))))))))))).))).))))))))).))))).....))). {-35.40 d=1.77}
 frequency of mfe structure in ensemble 0.387655; ensemble diversity 2.67  

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

Xtro_210532 secondary structure

Pair probabilities of base pairs in MFE structure

Xtro_210532 pair probabilities

pair probabilities

Positional entropy of base pairs in MFE structure

Xtro_210532 positional entropy

positional entropy
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