lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-505.70) is given below.

1. Sequence-
GCAACAUCUAUGUUGGAAUAGCCCCCAAACAUAUGCACUGUAAUAUAAAAAGUAAGGCCC
AAAGCAAUAAUACAACCCAUUAAUCGCCUAAAUGAACUAAAGACAAGCCCAAUAAAAAAA
AGGUCUUGGGCAUGCCGUUAUAUUACAAUAAAGUCUCGACUUUUAAUCAUAGUUAAUUGG
GUGGUACAUAGUAUGCACACAAGAGGAAAACACAUAUUACAUUUAGUUUUUAUUUAACUU
AGAAGUUUAUACAGUGACAAUCAAUUCAAUGGUAUAAAUAGAAAGGUACAGAUAAAUCAU
AAUAAACAAAUAAGUCAAAAAAAUGGGACUGUUAGGCUUAGAGAGCCAUAAUCCUAAGCA
CACAUGCAUAAAUAUAUAAAACCUUAUUGGACUUUAAUUAUCAUACGAGCCUAGUGAAAC
AAUACUAAUCCUAUGUAGUUAUGAAAUAGAUAGGAAAGCCAUGUUAUAAUUAAUCUAAAA
CUGGAGGGAGCGAAAACAAGCCUAUGGCCUAAUCAUUUAACCUAUCAGCAUGUAGGAUAA
ACAGGUCGUUGGUUUAGACAAUAGAGAAUGGAUUCAACACACAAAUGGUAAAGGGGUGGG
GAACAAGUUUAUAAAAAGUAAUAUCAACUCCGCAUGAAGCAUGUAGAAGUCCCAGGCUUG
UAACCAAAACAUAAAACCUAAGGGGAGAGGGAAUGGGAUCAACAGGUUCAUUGUGCAGCU
UAAUUCAACAUAAAAGGUGACAUAUUUGUUGAAAUUUCACGCUCACUCAAUAUAAAAUCA
AACAACAGGUAUAAAGAAGAAGGGAUAAGCUUAAUGCAAAAACAGGUAGUAGGUUUAUAA
UAAGAAAUAACAAAAAUCCAAUGUACCAGAAGGACAUAAAUUAAGUGUCAGGCUCAGAGA
AUCAGUAUGAUAUCAGUUUAAAGGAAUGGAAUAUGUAACAUGUUUUCACAGAUAACACAU
GAAACUAAAGAGAAGAGAAGAAGAUGUCAGUCUAGUUUAGCAACAAUUAAGGAUUGGGGA
AAAUGGAUCAGGCAUUCUCUACAUCAAAUAAUCCAAACUAGGUGCAAAGGAUCACACAAC
AGGUGUAUAUAGUAUAACAUAAGGUAGCAGGUAAGGUUGAAGGUGGAGAAGUCAUGCAUU
UUGAAAUAAGGCAUGAAUACAAAGCAUAGGGACAGGUAUAUAUAGAGUUUUAUAAGGUCA
CAUAACAUGCAAGUUAUCAUGUAAAAACAGACUAGAGCAACCACAAGUAAGACAGAACAA
GGAGCAAUAGGUAAACCUAGUCUAACAACUGUCACGUAUUUACAUUCUUUUAGGUAGAAU
UAAGCCAAUAAAACAAACUCUAUCUUAAUUUAUCAGGGUUUGAUAUCAAGUUUUACAUAU
GACAAUUAAGAGAACUGUAGAUAAGUAUGCUAAGUCAACCUGUUAAGAAAAGCAAACUGA
CAUGUAUUAUGACCAUCGAAAGGUUCACUUUGGCAGGCAAGAUUAAUUUUCAAGAGAUCA
UAGAACCUGUAUCCAGGCAUAAUGUUGCAGUUCAGUCAUGUUAUGAAAAUACUAAGACUU
GAAAAACUCGCAUAUAAUCAAGUUAAGACUACUACUAUAUUUCAAAUGACUAAUAGGCAA
CAAAGAGGUUACAUAAAAUAAAGUUGAGCCUUUAUUAGAUAGUCUAAUAGUUAUAAGGGC
AAACAUAUAUAUGGGUAGUAUCAAGAAAAGUUAAAAAGUAGAUCUCAGUUAUAACAACAU
UUAAUUUUAACACUAUUUUAGGAAAGCUUAUCAUGCUAAAAGUAUGUAAUCAGGAAAUAA
GAGUGUCACUGGAAAUAAAGCAUGCUUCAGUCAACAUUAAGCUAUCACUAAACUAGGAUA
AUAUAACCUAUAAAUUCUUUCUAGCCAGUCACAAGGUGCAAUGAAGCAUGUCCCAAUACA
AUCAAGGCAAAUAAACAAAAAUAAAAAGACAUAUUGUCUCCAACAAUACCGAAAAAUGGA
AAAUAUGAUUAGACUAAGUAAAGAAGAUUUUGAGAUUGAAAACGACUUAAAAAUAUGUGA
GAGGACAUUUAAAUAUCCUAUGUCCCUCAACCCUUUAUGAGUUCCUACCUUCGGAUUCCU
UGGAGAUAAGUUGGACCCCACACCAGCUCAUACCCUUCUCCUUAGGCACUCUGGCAAGAU
AUAAGAUACUGGGAAUGAUAAAAAAAUCAAGGGGAUUCCCAGAAUUAACCUUGCAAGUCA
ACUACCUUUUCCUUUCACUCAUUAAGGUCAUUGUGCAAUAUAGGCAAUGGUGGAAGGAGU
UGAUCAAGACCAAACUUUUCACCUCAAGCUAUUUUGAAACUACAAUAGAGACUUAUGGAU
GAUCUUUUAUCACAUGAGUCUCACACAUAGAUAAUUUUAAAAAUAGAAUAUGGGGUGAGU
UGAGGGUCUUUGCUUUAUGACUUUGGGGUGUCAAAG

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 [-549.89] kcal/mol.

2. The frequency of mfe structure in ensemble 7.28395e-32.

3. The ensemble diversity 463.47.

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