lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-270.70) is given below.

1. Sequence-
AAGACACCAUGCCCUCUUCAGAUCGCCGCUAUAACUACUGGACAUAGUUUACGAAGAGCU
CAAAACAGACCAGGUCAGAUGUGACGAAAAAAUGGAUAAAAAGACAAACAUAUUCGUAUG
UGUGCAUUAGUAUGCCUGCGAGCAUGCAGAGAGAGGGAGACCUAUGUUUCUUUGUUACAA
CAACAACAAAGAACCCAGUAUAUUCCCACAAAGUGGGGUCUGGGGAAGGUAGAGAGUACG
CAGUCCGUACCAGUACCUCAGAUGUGAGGUAGAGAGAUUGUUUCUAAUGGACCCAAAUCU
UCUAGUCUUCUAGGAAUGCAAGUAAUGUCAACCUCAACUUUCCGGAUGGUUGGCAGUAUC
UGCAUGGGGGUUAACACAUGCAUCAAGAGUAUAAUCAGCGCACAAAACAUGCACCGAGUA
CAUAGAAGGUACAAAAUAGGAUAUACAAUAGUAAAUGAUAAGUCCUAUGAAUAAUAAAUG
AUAAGUUCUAUGCAGUGUAUGAACAGUUAAUUCAACUUCAGCUCUAACGUAAUGAAGCAA
UUUAGCAGUUUUUAAUGAAAACAGUUAAAUAGCUCAUAUCUCAAGUAAUCUCAAUUGAAC
UAGCUCAAUUCAUCAGUUUUAACAAAAUAUAAAGACAGUUAAAAACAAACUUUCUCUUUA
UUUCUUUCAAAAUAUUUAAUUUUAUCUUCUCUUCAGGAGUUUCUAUAACCGAUAUAACUC
AAAGCAUAUAGAUAUGAAGUCCAAAAUUCACCCUGUGUGUAGCCCAUACCACACCACAGG
AAGGGACAUCUCUCUCUAGUGGAUCCAAUUGUAUGUAAGGCACAAUUGAGCGGUACCAAA
AUAACAUCCUAUGCUAGCUACGCAAGUUAAUGGGUAUUGAGACCUCCUCUCCCACCCUCG
GUACUAAUACUCUCACCAUAACAGCACUUACUUUAUUAUGCUUCUCUUUCACAUCUCAUG
AUUAAUGGAAUUCAACCUCGCGAAAAAUCACUAAUCAAACUAUAACAUUCAUUUAUUACC
ACUGAUCAGUUAAUUGCAGUCAAUUAGACUCUUCAUUACAUCAUACCUCUCAGCUUAUCA
AAUUACGCAUAAAAUCAUCAUCAAGCUUUUAAUUUUUUCAAAAUAGUCAACUUACACAUG
CUUCACAUUUAUAAUCUAACAUGUGAAAAUCAAAUAAAUAUGACACUUCAAUGCUCAAUU
UAAGUUCUAAAAGUAAACCUUGGAAUCAUCAAUUAUCUCAUGUUUCAAAGCUCUUUUCAU
ACUUCUACUUUAAUUUCAAAAACAUACUAACUCACGAGGACUUUCAUAAUUGAAUAAAUA
ACUUCAUAAUUAUAACUCAAAAUAUCAAGUAAAUCAUCAACUUAGGAAUCUUAGUUUAAU
GAAUUAAAUAAGAACCCUA

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 [-295.99] kcal/mol.

2. The frequency of mfe structure in ensemble 1.52308e-18.

3. The ensemble diversity 270.80.

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