lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-562.80) is given below.

1. Sequence-
CUGUAUUUUGACAAUCAAAUUUUAAAAUAAUAUAGAUUCAUUAUGAAUUCAACACCAAUA
CUGAUGCAAAAUUAAUUCUAGUCUUUAAACGUUAAACUACGAAACAUGCCUAUCUGCUAG
UAUUCAUUCGUCCCUUUUAGGGAUUCAACCAAGCAAUAGAAACAAGAUUAAAUGUCAGCG
UCAACAUGUUUAUAGAGGAAAAAAAAAUACCACAUAGAUAAGAGAAGUUUAAAGUUGGGG
CUAUCAGGCCAAACUUUUACGCUCUUUCGAGUUGUCUGAUAGGCUCCUACUGAGAUUCAU
UCCUCGUAUCAUGCGGAGUGAAUAGGGCUUAUGGAUCAUGAACACACCGGCAAAGAAAAA
GUACGCAAGGGAUACGCCUCUCCCGUUGGUCGAGUUACUCCGUUCCUCUCCUUAGGUGUU
GAAAAAAAAGAAUGUUGCUUGAUUGAACGAACAUUGGUUGAACCAAUUCACUUGCAUUCC
AGAUAGCACUACAAAAAAGUUGUGGCUGCAUUGGUUGUCCGAACUUUGAUUCAAAGCUCU
UCUUUCAGCUUUUUGAAAAGAGAGGGGCUGACUCGAAGUAUGCAAGAAUAUUGUGUUGCC
UUCAACGCUCUCUAACACAUAAUAUGGAAGAGAAGAGCAUAGUGAACUCAUGUGGUUGCC
ACAUGCAUCAAAAAUAAAAGAAUGAUUAGCAUAUCUAGAACUAACACAUAAUGGCUAUAC
UAGCAAAGAAACUCAUUUGUCAAUGAAAUAACACACCUCCACGAGGUGUCGAGAACAUAU
GAAACAAACCUUGAGGAUUUUAUUGAUCUAAGUUUGCAGAGAAACAUAGAAAAGGUUAAG
UUUAAACUAAAAUAGAUCUACUCAUAGUCCUUUAGCGAAUACUGGACAAUGAAUUAAAUU
CGCGUUUCAAACUAGUUAGGGCAAUAUAUAAAUUACUACACUUAAAAACACAUAUUGCUA
UAUAGAGAUAAGCACUCUAAUACAUACAAACUUCAUCUUGGGUUCACAGAGAAAAGAAGA
ACUAUAAGUUGAACAAAUUUACACAGUAGCUUGCGGGAACAAGAGAGUGAUCCAAAGUCG
AGCUUUUCUAAAUCCCAUUUGUGCUGAAUAUAUACUAUUUCAAGUGAAAACAAGCUGGAA
AGACCAAUCAAAGAAAAACUCCUUCAUUGUUCCAUACCUAAAGUUAUUCAUUCUACUUAA
AUCAUCUAAUCUUAUAUUUUAACCAUAAAUCGAAACUCCUUUUAUUAUUAAUUUAGAUUU
AAAUGAGGAAAAUGCCACUUGAAAAGAGGAAUGAAGCAUUUAAUGCAAAAUAAAACAAGA
ACAUGAUUUUACCUCAACUUCUAAAAAAAGGAGCUGCAUAUGAAAGAACCAAAUUCUUAA
UCUUACUGUUUAGCUAUUAAUAUCCAUGUAAUCUGUUAGAAAGCUGCAAGUUGAUCUUAA
ACAAAAAACACUUCAAUGAUUUACUAUAGAUUUAGUUGGACAAACUUUACGCUGACUAGU
UGACAUCAGGAGUAAUCUCUGAACUCUGUUUUUACCUCAAAGAGGACAAGUGUUAAAAAU
GAAUUCAUUAAAAAUAUCACUACUAUCAGCAUAUGCAUUUACAGUAGGCAUAGAGAGAAA
CUAUGUGCUAAUACCCUUCAUAUUUUCAUAUACAAAGAAGAGGAACCGAUAACUUAAAAA
UAGAUUGAACCAACCUAGAGAAAGAUAUCUAGUGACAAAGAACAUUAAGAAGGGAGGUGG
AUUUAUAAAGCAGGCAACACCAACACAAUCCAAAUAGACAAAGGGUAUAAUUAAAGGGGA
AAGUGCUAAAUGAUGAGAGGAUUACAUUAUAGCUAGAUUAAAAGAUGAAUUCUAGUUCUC
UUUAGAAGUCCACAUAAAGGAAGCAUGUGAUCAAAUCACAAGCUUAAAUCCAUAAGCUAG
UCUAGCGAAAAAUAAACGGAAUAAACUCACUAUCGAGUCACUUCUACGAAGCUAAACACG
AUGCCAUAGAUUUCUACAAAAAAUCAAUCAAUACAAACCAACAUCAUAUAAAUAAUCAGA
ACCUCGUCUAGAUACUAUAUUUUAGAUUUCCCGAACAGAUGAACAAAUUAUUAUAUUGAC
UUCAUGAUUUUCUGACCUCGAAAACACAACAAAAAAAUAACAACUCUUUAACACUAAAUA
UGAAAAUUUGAUUCCCCAAAACCCUAUAACCCUAUUUAAAAUAAAUUAAAAAAUUUACGG
AUUCAGGCCUAACAUUUUAAAGAACAGAACAAAAUGAAACAAAAUUCCUCCAGAGAAAGA
GUAUAUGAGAUGAUAACUAAGGUAAAGCUCAGUUAUAAAAUAGAAGAUUAAGUAUUCGAA
GAGGCAAAAUUGGAGAGAAGUUACCUGAUUCUGGGAAGCUAGCUGAGACAACGAGUUAAC
AAGGAAUUUCACUACUUUGGAUCAAAAUCCAACUUAUUCAGAUUAUAAAUGCUUAAUAAC
UGUGAGAAUUUUGCAGUCAGUAAUAGGGGACUGAUUUCAAGUUCGAAAAAACCUCUCCCC
AAAUGGACAGAAUACCAUGUAUUUAUAGUUGAAAACAUGGUUUGACACUAAAAGAUAUCC
AUUUGAGAAGAUGCAAGAGAAAACGAGUAUGGAAAAGCAUAUCGCAAAAAAUUCAAAUUU
AUUUGAUGACAACUGAUUUGGACAAAUUUUAGCAAGAAAAAUACAGUUCAUGAAUAAAAG
UAAACAAUGAAGGCUACGUGAAAUGGAGAGAGAAAUUAAAGGAGUUAGUAGGGGCGAUGG
UUAGGUCUCUGAUAGGGCUCAGGCAUUUGUCAGGGAGGAAGAAAGAUGAUGAUGAUGAAA
UUUUCCUGGCUUUUGGAAUGAUGAAAGGGUUUGG

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 [-617.79] kcal/mol.

2. The frequency of mfe structure in ensemble 1.78493e-39.

3. The ensemble diversity 692.34.

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