lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-393.70) is given below.

1. Sequence-
AUAACCCAAAACAUUUUCUUUUCAAUUUCAUGGAAGUGUUCGACUGUAUCUAAUCAAAUU
UUGCACUGUGACGAUGCUGCAUAUAAUAUGGUUCUGACAGUAAGUUCUGGUUUCAACGAA
AUCUCUUGACAGUUCAAUUAACAUUUGAAGAAUAAAAAUGAGGUUGUGUAGCUUAUUUAC
AAAUUUUGACUCAUUGAAAGAUAAUCCUCUAAAAUAAUGAAAGCAUAGUAGUAUAAAAUA
GAGAAUGCUAAACAAGACACAGGAUAAAACGGGGGAAAAAAGCCAAACUAUUAAGGGAAU
GUAGUUUAUUUAGGUAUACCUAUCCAUCUAAAGAAGAUUGUGCAUCCUCUGCUUGUUCUU
UUGUGUUAUGGGCCACAAAGUUGAAAUUGUGCACAAACUAAAUAGUCCAGGCUUGCUAAU
GUGGGGAAAAGGAUGUGGAGGUACUUUAACCCUCACCUGUUUUUGCACUUUUGCAAAGUA
AGAAACAUAGAAAAACUUUCUCAAAACUAAGUACCGGAGAAAGUGCAGAAGCUUGGGAAU
AAUGUGGUGUCUUUCACAAGGAUGGGAAAUGUGGUGUCCGUAAAUGUAAGUGGAACAAAA
AUAAUUCCAAAUUUAAUAAGAAUGCAGCUGGAAUGUAAACCCAGUGAUCAAUUUAAAGUC
UACAACAACUUUAGUCAUUGGACAUCACCUCUUACUUGAUUAGCUUCUGCUGCAAGCUUU
UUCCUGACAGAUCAAAUGAAGGCUUGACCUACACAUUUGCUAACGAAGUAGUAUGAUUAU
AUUUUCUAUCACUUGGCAGAUAAUAACCAACUUGAAGGGUUUGAGCGAUAAGUAUAAAAA
AAGUGGAUUUCAUGAAGUAUAUAUACAUUCACAUUAGAUCAAAGAAAACCAAUAAUACAA
UUACAUGUAUGCAACUUCAAUGUUCUGAAUUUAUUCAAGAACCAAAUCAAAAUAUCAUGU
UAAAUUGAACACAGAACUAAUCCAUAGAACUAUAUUCAAAUUAAACGAAUUAAUUAGCUG
AAGAUAAAAUACCUCUUGUACAAGUUACGGUUUAACAUAAGAUACCAUAAAGUGUUUUAA
GUAAUAUUCUCCAUCAGUGUAAAUAAUUUUUACACCGUCAAAUUAUCAUUACCUGUUUGU
CGCAGGUGACAUAUCUUAAUUUCAAAAUUCAAGUUCACAUGUUAAAGAGGUUUUACCUGU
ACAUAUCCUUUGAAUAACCUAUGUGUAAGAUAUUCUUACACUGAUGGUGUAUAAAAAUUA
UAAGCUCUAUCAUGAAAUCCACAAAGAAUUGGAUAUAUAUAUAUAGAAUUAUAUUCCACC
AGGAUUCCCAUGAAGAUUUCUCUUCUACUUAGCAAGUGGCUGCUGCUUAUUCUGCUGCUA
UUGGGAUUGUGAGCUGGAACCAUUGCUACAAGUAAUAGAAAAAAUAUUAUUAUUUGAAGU
GUGCAAAUGAGCUUCUUCUCCUGAAGAUAAACCGCUUUCUUUGCCUGAAAUAUUUGACAU
UUUGAUAAUAAAGGGGUGAUAAUAAAUGUCAGCAGAAAUGCAUACUGCAAAACACUUCAA
AGAGAAAUCAACAGAGCAAAAGUAACCUGUGUCAAACAGAUCUUGCAUCCAUGCAAAUUU
GAAGAUUGUACUAACUUCUUCAUCCCAUUUACGUUUUUAACACUACUGAUUCACUUUUUG
GUUUUAUUUCAGAUAAAAAGGCUAGCACGUCAAUAGAAGAAUCAGAAAGAUGGCACUGGU
AAACUUUUAGCAUUACUUAGCAGAUAAUUCUCUAAAGCAUAAUUUAAUAAGUUGAGACAG
GAUGCUGACAACCUCUAAUUGUUGCAUUCACUCUAAAACUAUUCCCAACAAUCUAUAAUA
ACCAAAAG

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 [-429.94] kcal/mol.

2. The frequency of mfe structure in ensemble 2.88944e-26.

3. The ensemble diversity 425.71.

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