lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-518.80) is given below.

1. Sequence-
AAAAGAUUUAGCUGCUAUAUAUAGGUAUAGUUUAGCAUUAAAAUCGUUUGUCAUUAUAAU
AAAAUUGUCCAAUGGAAAUGCUUUACCAAACCGUUGCAAUAGGUGCAACACUUUUAUGGA
ACAUAUUUUUUAUCGCAACGGUUUUUAGUUCCAUCAAUGAGAGGAUAUUGUGGUGUCUUC
UUCUUUGUUGAAAUAUGAGAGCUCUUCCAUUCCAUCUUUCUGUUAGUUCAACUGCUAAGU
UUCGUAGUUUCAAGUACAUUCCUAUGUUUGAAUUUUUCUAGGAUUAAUGUUUUUUAAGGC
UUUAGGCUACUUGAUUAUGGAAAGAGAGUUUUAUCAAAGUAUAUAAGUUGUGAAAUGGAA
AGGAGUAAGGAUCCCUAAGGUUGUUCCGAAUGGUGUUCAGUUUGUGAAUCUGAUGCGUAA
UCAUGUCUAGAUCUAUCAUUUUGUAUCUGCAAUGGGAUCCUCGGUUUGAUAUGUUUCUAC
GACUUGAGUUUGUCAAAGUAAGCCUGCAUCAAAAGACUUCGAUGGUUGAUAGUACCAUGA
AGAGACUUCGCAAGAUAAGGCAAGGAACGGGGAAAGAUCUUGAAUACCAUACCUCCAUUC
CUAAAACCUAUUGCUAUAUUUGCUUAUGAUGGGUAACCACCAGAAAUUGGGCCUAUGACA
ACAAUACUUUUACUAUUUGGGCCUAUGGCAACGGUUCAUUCUUUUCCCAAUGUGGAUUGU
GUCCAACUGUUUUAGUGAUUCAUGCCUCAGUAUUGUAUUGUAUAUUAGUUUGGAAAAUGC
UAAAGAAGACUUUUUAUAUGGAUGGAUCAUGAGACAAAGAUGUUUCUCAGCCUACUUCAU
UAUGUAGCUUGAAAGUUCACCUAUCUAUGCAAUUUUAUCCAUCAUUUCUCAUUGUUAUUU
GCUGACUCUGGCCAUUUUUUCUUAUUUUUCUAUCUACUCCUUCACUUUGUAACUUAGAUG
UGUGGUCUCACAUAUCAACAAUACCAAUUUGUUGUUAGCUCUGUUGCCUUCGAAACGCAC
UGUAGCUACAGGUUAGGUCUCUGUGUCUCUGUUGGGAAGUUAUCUUAUCCUAUUCUAGUG
GUGAUAAGAGACUUCUAGAUGAAGUGGUGAUUCUAUAACCACCCCCUUCACCCCAUCUCU
ACUGAUUGCUAAUGAUCACUUCGGAUAAAAAAGUAUAGAGAUUAUGGUUCAAAUUCAAUA
UUAGACCAGAGACCAAGUAUGUCAGAUGAUAUCUUUCCAUUUCUAAGUUUUGGCGGCGGU
GUUACCUCGAUUCAUAUUGACGGUAUAUAUUUUCUUUUAUAUGUGUCCAAUUGUAUUUGG
AAGUAUAUACCUUAUGAUCACUUCCUUAAGAUCUUGAAGGUGGUUUUUUUACAAAUACUC
AUAGUAGGUCUGUGUCGAAGAACAUUAAAUUAUGUGUUAUCCUGUAGGUAAACUUUUUUU
GGUUUAGAUUUCUUUAUAUUUUGACAUAUACAUGUGGAUUAAACGUAUGCCAUUUCGAAU
UUCUGCAUCUAUUGAUGAUUUCCAUCCUUCUAUUACUUUUUUCUUGUCAUGAUUUCUUGG
UAAAUAGGAUGAUCACUUAACAUGUUCUGUGACGAAAGAGGUCAACUUAUUUCAAAUAUA
UAAACUCAUUUCAUAUUGUAUAUAUUUGGAGUCUACUAUGCAUAACUUUUUCUUGUGCAA
UUAACAUAUCUAAUCACUGGAUCAGAACUUCUGCUAUUAACAAUACAAGGAGAAAUAAGA
AACCUUUUUUGUAACCUUUUCAACAUAUAUAUAAUAUGUGUGAACUUGUGUUACAUAUGC
ACUCAUAAGUGACAUUUCACUAAUGCUCUUCAGUGAAUAACCAGAAUAAGUCAGUUUCUA
GGUAUGUCCACUAUGGUUUUCGAGGAAUCCUUCACUGUAGGAGCGUUGUAUCCUGUUUGA
GGCAUUAAUCCUUUCUAAUCACUUGAGGUUCUUAUUUUAAAUUGGUUGUCACCUAAGAAU
GUUUUGUGAAAUGUCUCUGUGCGUUUUGUGAAAAGUAUAACCUUUUCAAUCUAACCUUUU
CACAACAGUCUAGUGUUAAAAGUCUCUGUAUGUUAAGCUAACCUUUUCUAUAUUUAGUUU
UCUAAAGUUAAGCAAAGGAUCUGAUAGUUAUGGAUAGAGAACGUCCUAUAAGAGUUGCAU
CUGGAUCACUUGCAUCUCUGGAAAAGAAAAAAAAAAAAAAAAAAAAAA

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 [-558.60] kcal/mol.

2. The frequency of mfe structure in ensemble 9.05208e-29.

3. The ensemble diversity 567.14.

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