lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-488.90) is given below.

1. Sequence-
AAAAAAAAUAAAGAAGUUAAGCUGCUGAAUACAAUCUCUUUUUGGCUACAUGAGCACAAA
AUUCAUCUCAAUUCUAUCCAAACUCCAGAUCCACUGCUGGUGGCAGCCAUUCUGGUUCUA
UUAUAUAAUACAUAAUAAAAUCUGCUGCUAAGCAGCAAACCGGUAUAAAGAGUUGAACGA
AGAUUGAAAAAAUCAUCCUAGAAAUAUGAAGCAACCUAGCCUGCACCACAAGUAGGAAGU
AGAAAUGCACAAAAAAGAACAGUAAGCACCUCAAUUCAAUAACUGCAAAGCCGAAAAUUU
AAAGGAAGCAACACAGCUAGACGAACUUAACCCCUGUCCUCAGAAUUCGUGCAAUCUUUU
AACCACGAGCAAUUAAACUGCACUGGUAAUUCCAACCCAAAAAUAAAGGUAGAUUACUUG
UCGAUUCUUGUCAGUGAUAUGCUUGGCAAGAAUGAAUGAAGUGUCGAUUCUUAUCAGUGA
UAUGCUUGGCAAAAAUGAGUGUGUUUCACAUUUAGUCUAAUGACCCUCAUGGUCAUUUAU
AGGAAAUACGCGACGUUUUGCAUUCGAGAGUAUUUUAGCAGCUGCCCCAAGUCAUUUAUG
ACUUGCUGGGACCGGUAGUUUAGUUCCCUGGCGGUUCGGUUGAGAAAUAUCUCAAAUUGC
AUGCUUUAGAGCCUAAAACUAAGUAUUCAUUGACCGAAGUCAACUUUCCUUCAAUACAAG
CUAGGAAUUAAUUUCGACAGUUCCAUUAGCUCCAAAAUUCCGAACAAAGUCAAGAUUGAC
CUCAAGUUGUGUCUCGGGGUUUUCUUUUGCAAUUUAUGCUCAUUUGUGGAUUUUAGUUAA
GUUUAAGGUCUAAUUUGGAGUUUGUGUGGUAUUUUGGUUUUCGGAGUAUCGGAUCGAAAU
UCUAGCGCUUCCAUCAACUCCGGAAUGAUGAAUUUAAGCUAGUUUGACCCUCGGUACACU
UCCCAAAGUGUUCGUGUUCGAUUUGAGUUGUUAUGUGAAAAGUUGUAAAUUUACUCGUUU
UGACUAAGUCUUGGUCGGGGGUCAUUUUCGCUCAAACAACCUCCGAUGUCAAUUUCGUCA
ACUCCGAUGAGUUCGGAAUGUGUUUUUCACAUAAAUAAAUAUUUUAUUUGUCAAAUUUGA
ACUCUGUUUCAUUUCCGAACCCCUAGUUGAAAUUCUUGAUUUUUGUUGUUUUUCUGAUGC
AUGCACAGACCGAUUUAUCGGUCAAAGUGCCGAUUUAUCGGUGAUCGAUAAAUCAGUAUC
UAACAAUUGCCAGUCACAAGGGAAUGUCGAUUUAUCGGCAUUUUUUCAAUAAAUCAGUAU
CCUCCCAAUUUGUCAGUGUACAGGGGAAUGCUGAUUUAUCGGCACAAGUGGCCGUUAAAU
AGGUAUCUGAGCCUUAUUUCUUCAGUUUCCAGCCAUUUUAGGGUAUUAUUUUAUCAACUU
UCUCUUUCGUUUUCACUUCAAUUUUGGUGCGAUUUAUCUUGGAAACUUUCCCAAACUCCG
UAGAAAAGUUCUCUAAAGAUCUCAUACGUGAUCCUCACUUCGGUAAGUAAUUUCAUCCGU
UGAAUUUCAUGAUAAUUAGAGUUCUUCCUCCAUUAAUGUCCUAGUCAUGAUUUCUUGAUU
CCUUCAAUUAUAUCCGAAGUUAUAUGGUAAAUCCUAGCACUUUAGGGUUAUUAUAUAUUG
UAGUAACGUUUUCUUUUCCGAAUUCAACAUAUAAUUUCGUAACGAUCGAAUCAUUAAGCC
CCUUCGGGCUGUUCAAGGGUCUUCUCUUACUCGAAUUGUGCUCAAGUUUACUCGAUUGUG
CUCGUUGAGAACCUCGUGGAAAAGUUUAUUUUCAGUUUCGAUGAGCGGGCCCCAUAGGCU
CAUUUAAGGCCCAGUCCAAAGCUUAGCAUAAUUUAUACUGUUAGACUCGUAAUGACAUAU
AAAAUACUUUUACACAAGUUUCAG

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 [-524.73] kcal/mol.

2. The frequency of mfe structure in ensemble 5.61773e-26.

3. The ensemble diversity 379.69.

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