lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-450.30) is given below.

1. Sequence-
GCUCGUCAAGGGUAGAUUUUUUUUUUGGUUCUCAAUCAGCUUUGUAUUGUUUAGUAGCUG
CUUUGGACUGUUAUCUUUGGCUGAUGGUCUAUCGGGAACAAUCUGUUUUGAUGUAGGAUU
AAGGUCUGUGUAAACUGACUCUACACUCCACAAGCCCCACUUUGUGGGAAUUAUAGUGGG
UAUGUUGUUGUCAAUCACCUGUAUAUUAAUCCUGAAUUAGUUGAGGCCGGUUAUAAGAAU
UCUUCUUUUUGGCAUUUUUUGUUUCUUGUAUUUCACUGGUCAUGAUGUUGUUGUUGUUUC
UUGUACAAAAUUUUGACUCCUGAAGUUGUAAGUAGUAAUUGAAUAGUCUGAAUUGAAAAA
AAAGACGACGAAAAAAAUAAAAUAAUGCCCAUUAUUAGUUUCAAUAAAUGAAUAAAAAGG
GCAGUUUUGAAUGUUGAAGAGAAAAUGAUGCCAUUUCUAAUGUUGAUUUAUGUGGAGUGA
UGAAAAGAAGAAGUAGGUUGUUAAUGAUCUUAAAGAGGCCAUUCGAUUCAUAGUACCCGU
GACCUCUAGGUCACAUGGCAACAACUUUACCAAUUACUCCAAGGCUCCCCUUCGAAUUGG
GAAUAAUAAUAAGAAAACAAUAACAUGAUGCCUAUUAUUAUGAAAAAAAAUGAGGAGAGU
UUUGAUUGUCGAAGAGGAAAUGAUCUUAAAGAGGCCAUUAGGCUCGUAAAGGUCAGAUUU
UUUGUUUUUCAAUCUACUGUGUAUUGUUAUGAUGUAGUUUUUGUUCUAUUACUAUAUGUU
GUUUCUUGUACUUCUGUUACUUUUUUUGUUGGACUGCUUUGGACUAUUUUUCUUGAGCUG
AGGGUCUAUUGAAAACAACCGCUCUAGCUCUAAGAUAGAGGUAAGAUUUGUGGACACCCU
ACACUUUUUGACCCCAUUUUUGUGGGAUUAUGAUGGGUAUGUUCUUGUUGGUUAUACGAA
UUCUUUUUAGCAUUUGUUGUCUCUUGUACAAUUUUUUGACUCCUUGUGAAGUUGUAGAUU
GUAGUAAUUGGAUAAUAUGAAUUGAGACGAAGAAGAAAACAGUAACAGGAUGCUCAUUAU
UAGUUGAAUGAAUAAGAAAGAGAAGAAAGUAGUUAUUGGAUUCCCAUUAAAGAGGUAGUU
CAGCUUUAAAGGUCAGAUUUUUUGUUUCAGUCAACUGUGUAAUAAUCCCGAAUUCGUUGA
GGUCGGUUAUAUGAAUUCGUUUUAGCAUUUUCUGUUUAUGGUACGAAAUUUUUGACUCCA
UGUAAAGUUAUACAUUAUAGUUGGAUAAAAUGAAUUGAAGCAAAAGAAGAAAACAGUUAU
AAGAUACCCAUUAGUAAUUUGAAUGAAAAGUAGGAUUGCAUUUUCUAGUUUAGUAGUUAA
CUCUCCUCGGUUGGUAGAAAGAUCUUUCCCUCUUUCAAUUCAUUAUUCAGGGUUUAGUUU
CAAGAAGAUUAACAACAAGAAAAAGGAAAAAUUAAAUCUCAAGAUCUUUUUUUUCAUGAU
GGUGAAAAUAUAUAGAACUUUGAUCUUUCAUGAGGAGCUGGUGGAAUCUUUAAAGCAACC
ACCAGUGAAAAUCCAUAAUAAUUAAUAGAGGUUUUCUUUUACUAGCUCUAAUGGCUAACA
UAGAUGUGUUUCUUCUGGAUUUCUAAAUGCAGAAAAGAAUAUAUAGAAUAUUACUAUUUC
AUUGUCCUACUUGCAUGUCUGAUAGUGUUGUCUCAAGUGGAUAGUGAAAUUUCAAGGUAG
UCGCAAAAUUGAGAGUUCAGGAAAGAAUAAAAGUAAGAGCUGAACAAAAACCACUUCUAG
UAGUUUUCUUAGGUUUCAUGUGGAUAAGCUUCCCAUAAGCUACAAAUGUGUAUGCUUCAA
GCUCA

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 [-486.39] kcal/mol.

2. The frequency of mfe structure in ensemble 3.69484e-26.

3. The ensemble diversity 360.21.

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