lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-360.20) is given below.

1. Sequence-
ACAAAGUGGGGUCCGAGGAGGGUAGAGUGUGCAGUCCGUACCACUACCUCAGAGUUGAGG
UAGAGAGGCUGGAAAUUGUUUAUGUUGUCUUUGAAUUGUCUGGAGUUGGUUUUUGGGAAG
GGAUGAUAUAUUACUGAAUAUAUCAUUUCUUCUGGAUUAUGUUCAGUGGAAGAAUGAUUA
UGAUAUUAUGAGACGAGUUAAGUUCAUUGUUAGCAUGUUCGUUCUUUCAAUACUUCUCCC
CCUUUUUGCCCGUCCCUUUUUGAGGUGAGCAUAGAGGAGUGAUAGGCACCAUUCUUCGAG
GGAUAUAUUGGAAUGACAAUUUAUUUCUUUCUGGUGAUGAGUAGCCUUUAUGUUCUGGUG
AGGACUAGGUAGAUAAAUCAUACAACAUAAAAUGGUCUUUGGAUUUUAUUGAAAUUUAGU
UAAUAGUGCUCUCUCUUCACCCACUUAUGUUGUCGAGGGUGGCUCUUCUAACCCCAAGCU
AUAAUUGCUAUUUAUAAGCAUUCUGCAUAUGAAUUAUAAGCAGUUUAAGCACAGUGGAGG
CUCCCUUCUUUUCAUGCUACAAGUGCUGGGCAGUUCAUUGUUGGUGAAAGUUGUAUAUCA
AGGAGAGUUUAGCACUAAUAUUUUUCAUUUUAGCUAGAAAAGAGUCUGGUGUUUCUUCUG
GAAGUUUAGGUAAGUUGUGUCCUGUUCGUAUAGCAUGUUUGGUUUUUUGGUUCUAAUAUA
CAUCUGAUAACUUUGAUAUUUAUUAUACAGCUGCAUGAGUUGAAAGUUGUUCUCUUACUG
CUUGAUAUUGGGCUUGAAUUCAAGGGAACUUUUUAAAAGAGACGUUAAUAGUAUGGUGAA
CUUUCAAAAUUGGUAUGACAACAUGAAUUGUUACGUUGAAUUUUUACGUGUGCUAUAUGG
GAGAAUUAGGAAUCAAAUUCUUGGAGCGUGAACCUGAAACGCUUGUGCUUAAAGGAACCA
AUUGCUAUUUUACUUAUUCCAAAUGGAUACUUAAUAACCCAAUUUCUUCUAUUUAUGCAU
UCUCUGAGUAUAUCAUUAUUACAUUUUGCAAGUUAUGAUCUCAAUGUUGCAGUUGCUGCU
AAAGAAAGAGAGAGAUUCAUAUUGGGAUUUCAGUAUGAACUAUAGAAAGAUGAUUCAACA
UGCUUCAUAGUAAAGAAAAGAGUGCGAGAUCUCAGAUCUAACAAAGGUUGCGAAGUAUUC
CCAUUGAGACAAUCUUGGUCUCCUCACUGUUGAAAGAGGGUAGUUGCUAGAGCUGGACCG
AUCAAAGAUUGACUUUUAUGAUCGAUCCUUUCUCCCAGUGUUCUCUCUAGCAUUGUCAAA
CGUAAUCAAUUGCAGAUAAGCUCACAAGUAUGCCUUCCAGGAAAGAAGAAGCUUGCUCGC
AAGAGAAUAACUGG

2. MFE structure-
...(((((((....((((((((((..((((((.....))))..((((((((....)))))))).((((((........((((((((((...(((.((((((((((..(((..((.(((((((((((((((((....))))))))))))))))).))..........(((((((((((.((((.....((((.((......
.))))))......)))).)))))))))))..))).)))).(((((.(((...((((((...)))).))))).))))).((((.((((((((((((..((((((((.((((......)))).))))))))...)).)))).)).))))))))..((((((....)))))).)))))).))).))))))))))..))))))(
(((((((...))))))))....))..))))))).)))..)))))))...(((.((((...(((((((((..((....(((..((((((((((((((.(((...))).)))))))....)))))))..)))(((((((((((.((.((((((((..((((..((((((((((...((.((.((((((.........)))))
).))))))))))))))..............))))..))))))))...)).)))))...(((((...((((((((..(((....((((....((((((....(((((..((((((((((...(((..........)))...)))))....(((.((.(((((((.....(((((((((...(((((.(((.......))))
))))..(((.((((....)))).))).(((((((.(((((..(((((........((((((......))))))..)))))..)))))..))))))).)))))))))......)).))))).)).)))..))))).)))))...)))))).....))))....)))...)))))))))))))(((((((((((..(((((.
................(((((((.((((...(((((.(((..........))).))))))))).....((((...)))).................(((((((((....)))))))))(((((.(((..(((......)))..)))))))).......))))))).(((((...)))))......)))))..))))))..
)))))(((((.......)))))..)))))).....(((((((..((((.((((((((.((((((.(((......))).)))))).))).......(((((((......)))))))......((((....)))).....)))))...)))))))))))..))..))))).))))..)))))))............

You can download the minimum free energy (MFE) structure in Vienna Format

II. Results for thermodynamic ensemble prediction

1. The free energy of the thermodynamic ensemble is [-386.17] kcal/mol.

2. The frequency of mfe structure in ensemble 5.04253e-19.

3. The ensemble diversity 340.53.

4. You may look at the dot plot containing the base pair probabilities [below]

Download Dot plot JPG EPS

III. Graphical output

1. A note on base-pairing probabilities:--

The structure below is colored by base-pairing probabilities. For unpaired regions the color denotes the probability of being unpaired. The reliability information of RNA secondary structure plot in the form of color annotation, Positional entropy ranging from red (low entropy, well-defined) via green to blue and violet (high entropy, ill-defined).

Download RNA structure JPG EPS

2. Here you find a mountain plot representation of the MFE structure, the thermodynamic ensemble of RNA structures, and the centroid structure. Additionally we present the positional entropy for each position. The resulting plot shows three curves, two mountain plots derived from the MFE structure (red) and the pairing probabilities (black) and a positional entropy curve (green). Well-defined regions are identified by low entropy.

Download mountain plot JPG EPS