lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-376.64) is given below.

1. Sequence-
GAUGGAAAGCACUAAAAGCACUACCCGAAAUGCAUGGAGGAGUUAUGGUAGGAUUAUAAU
UGCCAUAAUUAACUGCAUCGUUGGGUGAAACGGAAAGAUAGAACCCUCUCCUUAAGGGGC
AUAAUAGCAUCUAUAAAAGGGGAGGCAAGGCCAGGAGGACAGGUAUGCUCUAAAUACUAC
UCACAAUAUUCUUGGAACUCUCUUAUUUGCUUAUUACUAACUUAAGCAUCGGAGAACUAC
CCGGGGACCACCCUGGGCUCUGUUUUGCAGGUAAUAAUUGUGAUUCUCAUAUACCAGACG
GAGCAUUGCACGUUGUGAGCUUGAUAAGAUUUUCCGUGACUUAUCAGUUAUUAAGUUAAA
AACAAAAAAUAUUAAAAGAAGUCAAUCCAAACACCAUGACUACCCUUUUCCAAGCUACAA
CCAAUUAAUGGAAAAACUCAAGUUACAACAGAACAAACAAACGGGUACACAAACGAGUUU
AUACACAAAUGUUUUCUCAGUUUUCAGAUAGGGUUUGUGUCGAGAAUUAAGAAAUACAAC
CUUUCAAGUGCGCAGAUGUUUUGUUUUUUAUGUUAUCUAGCACAUGGUACAGCUCAGGCA
UUACAUCCAAAAUAUGUUUUGUCCGACUAUGAUAAAUAGUUACUAAUAUAUAAAUGGGUU
CAGUUUCAGACAAAAGUACUAUAUAAUUGGGUUUAAAGGACAAAAGUUUGAGGAUCCACC
AUGUUGCUGGAUGAAAAUGGAAACAAGAAAGAAAUGGAUUCUAUAGGCACAUGCCACAAG
AUACUUCAGAAGAUUAAAAUAAAGCAACGCAGGAAAAUUCUCAGCUUAUAAUAAUACAAC
AGUACAAAGUGCAUAAGACUGGCAUCUCCCUGUAUUUUCAAGGUCAGUUGGCUGACUGUU
UAAACUUUUAAAUAACUUGAAAUUAUAUACAUAAUCCAAGACGACUAGUUGCCAGCUCCU
AAAUGGAGUAUACUGUUUUUUCUCUUAAUAACUUAAAGUGGAGUACAUAUGAACAAAGUC
UCCAACAUUUAAAAAACAAUGUUCUUUCGAUUGAAACUAAAAUAGUACAAAUGAUAUACA
AAUACACAUAGAAAGGACUAAUACAGAGUAGGGUCAGCUCAAUGACAUUUUUGAUCCCUA
GGAUACUUAUAUGACACUACUUUUACAAUAAAAAUAUAAGCUCACAUUGUAUAAUACACA
AAUUCAAGAGAAUCCAACUCCACAAGUAAGGUUGCAGCUAGAUCAGGCUAACAUUAGUUA
CAUUUAUCUCCUAGAUUUUGUAUACCUAUACACUAAGGCUAUAGAAGGUCAAAAUGAGUG
UCAUACUUGACAUGAAAGAUUUCUUACUGGGUCUACUUCAUAGAAGUGCUCUAUACUGGA
GAUGGGCAAAUACAAUCUGUUUGGGCCUAACAUAAUUAGAAGUUGAGCUCUAUAUUGGAA
GCCUUACCAUAUCAUACAACUUAAAGCAGAAUGACAAAACUGGAAAAUCUUGGUCAUGGG
AGUGCUAUGAAUACUCAACGAUCCAUGAAGUCCUCUUCUCGUACUCCGGUUUUUCCCGGG
UUACACCUUGGAAUAGCAGUUCCCAUAUAUGAUCUCGCAGUGUAACCAUUUGUUCAAGCU
GUUCCAGUAAUCAAUCUUUC

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 [-406.18] kcal/mol.

2. The frequency of mfe structure in ensemble 1.52305e-21.

3. The ensemble diversity 392.06.

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