lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-402.14) is given below.

1. Sequence-
AUAAGGGAAUGGGAAAGAAACUCCAUUUGGACCGAGUCUAAUACUCCGAUAUGGGGCCAU
AGACCAUGCAAGGGAUCCUCAGUGUUACACAUGCAAAGAAAAUAAAUAAAUUAGGAAUCG
ACAAUGCUACAUAAUACAAAUAAAAUAAACAAACUAGCAAGGCUUAAUGCAAAACAUAAU
ACAAAUAUAAUUAACAAACAACCAAGGCUAAAUGCAACAAAGUGUAGAUUGGUCCAGCAC
CAAAAAAACACAAUUUGAAAAAAAAAAAAAAAAACAAGUCAACUAACGGCUCAAGACAAG
UCUAAGUUAAUUAAUGGAAACUGGGCUAAGGAAGAUACACGCCCCACUAAAUUCCUUCAA
AAGGAACUAUAAACAAUAUGGGCCAGUUGAAUUGCAUAGUUGCAGUCCGGCACAAUUGCA
AAAAAAGGAAAUGUCCACUUAGCAUAAUUACUUAACUAUCGAACAUAAUAACUAAAUUUU
AAUUUUUUUAGCCUUAGGUAAUAAGGUGAUACACAUGGUAUACAUAUAGAGAUAUCAUGA
AGUAAUACAAGUAUAAGCGUUUCUAUUUUCAUAAUCCAAAGACUAGUAUAAAGACAAUAU
AUUAGAGGGAUGUGGAGAGAAGGGAACAAGUAGAACAUGUUGCAUAAUUUAUUCAAAAGG
AUGGGACUGUUUGGCUAAAAAGACCAAGUCCCAAGCAAGUAGACAAACAACAUGCAUAUA
UAUUGCACAAAAUACAUUACUUAAACUAGAAUUAGACCUUACUUAGCAUGAUUAUCUACC
UAAAAUGACAUUAAACCUUUACAGAUAACAACCAGGUUAAAGGGUCAUGCUAAGGUUCAG
UUUUAAGAUUAGGGGAGGAAAGAGGCAAAUAUAUAGUCUACUUAAGGUGUAAGCACAAUU
AACAUAUAAAAGAAGAAAAGGCAGUAGAUAGCGUAGAAACAGUAUAAACUCAUGUCAUAG
AGAUUAAAAGAAAAAAACAACAAAUUUAUAUAAAAGAAUGCAAGUUUAACACAUAAAGGA
AAAUAGGAUAGAAACAUAUUUGCAUCAAGUUUAUAUAUAAGAGAGAGAAGAUAUCAAGUA
GGAACAUGAUCUUAGUACAAUGGGAGAGUGAGAAUACAGGCAGUAGAUUUACAAUAGAAU
ACCACAAACUCAAACAGAAGGAGAAGAAGAAGCAAAUAACAAGUAGGUACAUAGACUCAA
UGCAUAAAAGGAGAAAAGAAAUAGGCAGCAGACUUAUAAAAGACUUCAUGAACUCAAUAU
AAAAUAAAGAAGAUAAUAUGUUUAUAGAUAACUCAAUAUAAAUAGAAAGGCGAAUAAGGU
AUCAUUUUAUAGGAAUGAACAUUAAAUCAAUAUAAAGGGAAGGGAUACGAGUGACAUCUU
CACAGAAAGCAACAUCAACUCAGAAUGAGAAUCAUAUAGAAGGUUCACAAUUGUAAUACA
GACUCAAUAUAUAGGGGAAAGGGGAAGGAUAAAAUAGGUUUAUAAUGUAAUCUAAUUCAA
GACAAAGGGAAAAUUUAAGGAAUUAACAUAUGAAAAUACAAUCUCAAACAAAGGGAAAGC
GGAAGGAGAUAGUAGGUUAUACCAUAAACUAAAAAUAGGAAAAGAGAAACAGGAACCAGG
UAGAUCUAUUAGAACUAGGGGGCAACAAAUAUGGUCAAAGGGACAGUCUACACAGGAUUU
GAAUAAAAAAAUCUUUAGAGUAGGUUCUCACAUGUAGAAAGCAUGUAACUUUAGGAAUAA
GAUUAAGGUAACUACAGAUAAUGCUACCUUAGCAAGAAGCAAUAAAUAUUACACCCUAGG
UUUUUUAUAAAAUAGGUUUAGGACCUAAUAAAGAUGAACUCUAAUUUAGUUACUCAAAAA
UGAACAAGAAUUACUAAGUCUCUAUUUAUAAUACAGAUUCAGUUAAGAAAAGAGGAGGCA
GAUUCAAUAUAUAAGCUUUUAGGAAGAGAAAACAAGUAAGCACUAUAGCAAUUUCAAGGG
AGGGAUUCAUUGAGCAGGUUACAUCAACACCCAUAUCAUAAGAACACUUAUUCUAUGCAU
GGAAUAGUAGUUUUAGAAUUACACCUUAACUCACAUGAAAAGACACUUGGGCUUAGCCAA
UUAGAUAGAUCAAUUGAAAAGAACAGAAUCAUAAAUUACUCUUAAAAGGUUUAGUAGGUA
GCAAGGAGUUACAUGUAAUCAGGAAAGAUUUUAGUAGGCAUUUAACUUGUAUAAACAAUG
CAAAACCAGUUAGUAUGCUCAAAAUAAGCCACCUAGACAGUAUGCUUACAACAAGAGUAG
AGAAAAUGAUUUGCAUAUGAUCAAACCUAGUACUAUAUAGUUUUAGUCCAAAUUCAAGUA
GCUUAGAUAGUCAAUCCAUUACAUCAAGUUGAAGAGUUAUAGUAGUGAGCAUAUAGAAGA
AAUUACGAACUUUUUGUUUAUUAUCUUAAUCAAAG

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 [-446.04] kcal/mol.

2. The frequency of mfe structure in ensemble 1.16275e-31.

3. The ensemble diversity 592.78.

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