lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-314.40) is given below.

1. Sequence-
CUCUUUUAAGCUGAGAAUUGCAUGUCCUAGGUUUGAAUGCUCUAUUUGAACUUUACCCUU
CUUAGUUGUUCAUAUUAUCCCUAGCAUGUGAUUUAUCCUCAACAUGUCUUUAAUUAUAUC
UCUUAUGUAGAUUAGUUCAUUCCUCAUACAAGUUUACCUGGUCUUGUGUGCUUGCUUGCC
UCCUUACAUAUUGUCUGAUCACCUGGGACAAUGCUAACUAAUUGAUUUGUAUAAUGCAAG
AUGCACCUGGUCAAUCACAAUCUCUUUGCUGCAUGUAAACAUGUUAAGGGCCAGUAAUAG
UAUAGUAGUUCUUUAUCUAUGAGCAAAAAUGAAUGAAGUAUCCACUCUCAUGAAUUUAGA
AUGGUCUAUAAAGUUGAUAUUAUGCCCAUAUAAUAGCUUAGUGUAGUUUGUUCACUAUUC
CCUUACUUAAAAUUAACAUUUGUCUGGGUUGCCUUUUCUUCUUAAAGUCUCAUAUUGAAU
UUGCUUGUCUUCCUAUCCACCAUAUUUGUAUACAAAGAAUGAUUGACUUAGAGUAGGAUC
UCCUAUACUUCAGUUCAAAUAUGUGAUGAUAUGCUAUUUUUUUUUUUAUAUUCUCUAGCC
UCGCCCCCUAACUGUUUACCCAUUGUCUUUUUGACUCGAGUACUCGGCCUGGUUGGUGUG
UGCUUCUUCUUAUUGCAUGUAGUCCUGAAAUUUUGUAUUCAAAUUCAUGUCCCCUACCUC
UAUCCCACAUGAUGUGAUGCUUCUGGCCUCUAACUUGAUGAUCUUAUUUUAUUCCAUCCU
AUCUAAAUCUUCUUUGUUAUAUGACUACCUAAUUUAGUAAUCUAAGAAUUAAAAGAAUGU
AGGAAUGAAGAACUUAAGUGCUCAUAUUUGUCUCUAUAUCUUUUUAAGGAUAGGCUCUAA
AUACGUAUGCUUAUUUAGUGUAUAUGAGUCUGAUGAGGGUUAAAGUAUUAGUGGCUGUAA
UUUAGAUCUAUAAUUGCUUUAACUUUGUUCAUCAUCAGGCACUUAUGUGAUUUUUGUGUA
UAUCAUACAGACCAUAGAGACAAUACUUGAUUAUCACCCUUCCAUGCUAAGAUAAAUAAA
AAUAUGAGUAACUGGGCUGGAUGUAUAUUUUUCUGUUAGUCUGUUGGCCUGGGCCGCUUU
CAUGUACCUUAGCCUAUUUUUUUGGUUUGGGCUUGUAUUAAGGUCCUCUUUUUUUCAGUU
CUUUCCAUCCUUUGCUUCUCCACGUGGUUGUAUAUUUUGCCCGUAAUGGAUUAUACGAAU
UAUAAUGUCUUUAUUAUCCUUUAGUAUUUAUUAUAUUCAUUUGUGUUACGUUUUGUUAUC
AAUUUCUAAUCCUUUUUUUGCAUGUGUAACCUUGGGAGUUGGAGGGAGGGUGUUCGGAGU
CCUUUUUCAUGGCUUGAUUGGCUAUGGCUGUCGUUCAAAGAACUGAUUGGGUCAGAGGGA
ACUGUGAAGAGUUUAUUCCUCUCUCCCUUCUUCUACUAA

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 [-343.17] kcal/mol.

2. The frequency of mfe structure in ensemble 5.30535e-21.

3. The ensemble diversity 443.29.

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