lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-374.40) is given below.

1. Sequence-
CUUGGAGAGAGAUUAUAUUAAAUGGGAAAGGUUUUAUAUAUAGAUUGAUUCUUGAGAGUC
AAAUAGCCUGUUUUUGCUAUUCAAAGAUUUCAUCUUCUCUUUCAAAACAGGGUGUGGAUA
UCUCAAAUGUUGUCCUAUUUCUCACUCUCUUGCACGAAGGCACAUUUCUCAUUCUCUCAA
ACAACUAAAUUUUGGGACAAUCUAAAUGGAAGCAACUAAUUUCUUGAGGUAUUUCAGAUG
AAGAAAGCUGGAUAAACCCUCUUAUUUUAGGGUUUUCUGUCAAAGUGAUUUUCUUGAAAU
UUGAGAAAUCUGUGAGGUUUUCGUUAUCAAUCUGGAGAUUUUAAGGUUAGUGUAUUUUUC
UUCAUCAAUAUUUGAGGUUUUGUUCUUUAAUUCUGGGGUUUCAUCUCGUUAGAGUGUUCU
UAACCCAUAUUUAUCUUGAUGUUGGAUUUUGUGUUGCAUGAGCUAUUAAGCCGAGUAGUG
UGGGUGUAACUUUUUGUUGGUAUUAUGGUAAAAUCAUUUACUCUAGACCCUAUUUCUCUU
AAUAUUGUUGUUGAAUUCUUGCAUGAGCUAUUGGUACUGUGGGUCUAAGAUCAUCAUUGU
UUCUGAUGUUUUUUUUUUUCUCUUUUUCUCAUAUAUUUUUUAGAAUCGGUAUGCCCUAUC
AAUGUUGGGUUGUUGUAAAGCCUUUAGAUUAUACAAUGUGAUUAUGAAUUUCAUAUCACA
AGGUUAUGUACUGUUUGAGCAUACUAGAUAUUUAUUUGUUUACGAUUAUGUAUUAUUUUU
GGUAUUUCAAAUAAUUGCUGAAAAAUAACUUGUUAUAUAUUUUUUCCAGUUGAAACUUUG
UCCUUGUGACUAGCAGAACAUAGGCCAUAACUAGCGUUAAGUCCAGGACAAAGUUAACAG
UUAAUGAGUGUAAAUUAAACUGAGAUAAAUGCAGUCUUGAUGUGUAUUUUGUGUUAUUCA
UGUGUUGUGUUGUUGAAUGCUUGGUUCAUUAAGAUGUGAAAUGGCUUCUUAAUUACUCGU
UUGUAAAUAAUAGUUUAGGCUUAACUAAAAGGAAUAUCCUCGUGUGAAAUCUGUAGCAAU
GACAUGCUUUGGGGACUUUGGCUAGUCAAUUACCUUUUCUUGGUUUAAAGAUGCUCUUCU
CUAGAUGUUUAAAAUAAGUACAUUUUCUGUUUUAAAGGUUGUCAUGAUUUUACUGUUUAU
UGUUUAAAAAAUGAAGUAUAAGGGGUCACGAGUGAAUUAGGGCUGUUGAGUGUUAGAAAC
UAGCCUUAGUAUCUCUUUCAGGAUCCAUUUGUUGUUGUUCACUGUCGUUUGUGUGUUAAA
UUGGGGUAUUUUAGGUGAAGAAACCACAAAUUUGUGUGCUGGCUGCAUGUUAGCAAAUAA
AAAAUGGUGUCAAACUGAGGACAAGCCUAAGGAAAAUGGGGAACUUAUAUGAAUUAGUUG
UCUUAUUGGUAAAUACUUGUGUCUGGUUCUGUCCAUUUUGUUCUAGAUUUAUAGCAAAGA
AUGUACAUUUUGAUCCUAGCUGAUAUAUGGAGCACCUCUUGCUUGAAAAUAGAUGGCUCA
CAGUUGAUAUUUGGUGCUAAGUGCUGAUAACUUGACCUUUUUUUAAAUAAGCUAAACCUG
CUGCUAGUACCAUUAGAUUUAAGGAAUGUUUGAUCAUAAGGCUCUUACCUGAACACAUAG
UAUCUGAGGA

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 [-411.87] kcal/mol.

2. The frequency of mfe structure in ensemble 3.94714e-27.

3. The ensemble diversity 420.82.

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