lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-530.77) is given below.

1. Sequence-
UGAUAGUUACCUACCUGGUUGUUUAGAUAUAAAAUUUAGUAAAUUGGGAUACUUUAGGUA
UGGUUUUGGCCAUCAACUCUUAUUAUUAUUAUUACUACUACUACAACAUUACCCAGUAUA
GUCCCACAAAGUGGAGUUUAGGGAGGGUAGAGUUUAUGCAGAGGUUAUCCCUCGGGAGAU
AGAGAGGUUGUUUCUGAUAGACCCUCGACUCAAGAAAAGAAUGGUCCAAAGGCAGUAAUG
GAAGUGAAAGCAUAAUAAAAUGUAUUGAAUAGUAACUACAACAAAAUACUACGGCAAUCU
AAGUAUAAGAAACACAGAUAGUAACAGAAAUCAAAAGAUAAGAAACCACAAGAGCAAUAC
CAUGAGUACUAGUAUGGAGGAUAGUAGGACAACACACUGCCCUGCCCUUUAGAACCUGUU
AUCUAAGUUCAUGUACUCGAUAAGUUGGAACUGCGUCAUAUCCUGUCUAAUUCACCUCUC
ACCAAUACUUUUUUCGGUUUACUACCUCUCCUGAAAUCAUCCAUAACCAACCUCUUACCC
CUCCACACCAGAGCAUCCAUGCAUUCUCCUCUUUACAUGCCCAAACCACCUCUCACUUCC
CACAUUUUGUUUUCCUGAAGCCGCUCUAACCUUGUCCUUGACAUCCUCCUAAUCUGUGAG
AUCGCAGUGCAAAGAAAUAUGUUUAACCAAGCAAAUUAAGAGGAGAAUGAUCUCCAGGUG
UAGUAAUUAGCAUGUGGGUCGUUUAAUUGAUGGCGGGAGAUGGUCACAGGGACAAAUAAG
ACUUAUCUCUCGGAAUCAGUGUGAACAUAGAUAAGAAUAUAAUAUAAAGAAAGCAAACGA
UUGGAUAAAAUUAGAAACAACUACAGCCAAUAGAAGAUGCAAGUAGCACAUAUAGAGAAU
AAAUGAGUAUGUGUCAUUUGAGAUGGUUUGACAACAUCCUAGAUAGAUCUCCAGGUGUUG
CAGUUAGCAUGUUUGAUGGCGGGAGAUUGGUUAAAGGUAUGAGUCGGACUUAUCCUCUAG
GAAUCAAUGCGAACAUAGAUACGAACAUAAUAUAAAGAAAGCAAAGGAUUCAUAUAAGCA
GCAUCAACUAAUUAGAACUUUGAUUUUGUUGCAACUGUUAUGUGUCUUGAAUUAAGAUUC
AAUAUCCGUGAGGAGUCUUCUAAUUUUGUCUGGAGAGUUGGAUAAUGUGAGAUCUAGAGA
GCUACUUAUUUGUUGUAAAAGACAAACUAUUUAGUGUUGAAAUGAAAUAGACCCUAAAUG
GAGUAGAAUGGAUUGAGAUUUCUUGAUAACAAGUAGAAUAAAUAAAGAUUUUCAUAUAGU
AGAUCUGAGCACAUUGGGAUUGAGUUUAAUUGAUUGAUUAUGAGUUUUUCAUUAACACGA
GGAUGAUGGCCUCUAUCGAUAUUAUUGUGCAUUUAUGCUAUUGAAUAAUGUGAGAAACUG
CUAUAAAAGAAAGUGGAGCCUCUUAAACACUCAUAGGAGAAUAUAGUAAAGGGAAAUUAU
UGGGAGGAAAUUGGAAAUUCUGAUAUCCAACCAGAAAUUGGCAUGCAACUCACAGUGAGA
ACUAUAUAUACCUAGGCCUUUUUUGCUUUGAGCUUUGUAUUUCCGACUCUCAUUUAUAAG
AGAAGUCAGCUACCUUUUAUGAAUUUAUUUUUAUUUCAUAUAAUAUUUAUGAGCUGAGCU
UAAAUGGAGUAACAUGGCCAAUGAGGAUUCAUAUAGUUUGUCACAACUUGUUUGGGAGUG
AGUAAUAGUAGUAGUUAUUGUUAGUUUCCUUUCAAUACUUUCUAUUCAAGUUAGUUACAG
UUAGAUACUCCUGUUGACUAACCAAUAAAUGGGAAGUGUAACGGCCCAGAUCAAAUUUUG
ACUUUCAGAAAGCUUUUCAUAAUUUUAUCAUUUGCCGCAGUUUCUUUGACCUUUUAUGAA
GGCUUCUCAAUAUUAAUAGAUGUUUCAACUUUCAUGACUCUGAUCUUCCCAGGGUUUUGG
AAAUUUAGCAAGAUGAUUUUGAGUUGAGGGGUCUUGCUGAAAUGCUGCAUAGGUGAUGCA
UGAUAUGAAUUAUAUGUGCCCACUACUUCCACUAUUACCACAAUGUUUUCGUCGAUGCCC
UUAAAUAUGACAUGAUGGUGGGUUCUCAUUUACCAACGCCACUGAUAUAACUUCCCUGAG
AGGACAUUUUGUUCGGAGAUGACAAAUAACCUGAUGCCAGAUUUAUGAACUUGUGCCCAU
AGCGUGCAUAUUUAUUAAAUGACAUUGACUUACUGUUGCCUUUUCCCUCUCUUUUGAUAA
CUCAUAUCAGAGUUCACCCGGUAAUAAUUUGCUUGGUUGGUGUACUAUUUUUGUGACC

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 [-571.40] kcal/mol.

2. The frequency of mfe structure in ensemble 2.34316e-29.

3. The ensemble diversity 574.98.

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