lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-459.34) is given below.

1. Sequence-
CAUCCGCGGAUUAUUCAACUGUUGCCAUUGAAUCUCCUUAAAAUUGUUGGUGAAAUUAAU
UUACAAUUGAAAAAUUACAAUAAAUAAAAUACUUUCAGGUUAAGGCGCGAAUAUCUCACU
CUCUUUAAGGAGAUUCAAGCCCACUGUAACAAGGUUUUCACCGGUCCAUCAGUAAUCUUC
UUGACUUGUUCCCUCCGGAAUACAACAACCUACUCACAAAGUAACUCAAUAACUCUGGAC
AAGAAUUGAGUCUCAAGCUCCACACAAAGAACACUUGCUUUCAAAGAAUAUACUCUUUUU
UUUACUAACUUUAUGCACUCUAUAUUUUGUGUGUAUCCCAAAACAAUGCAAGUCUACCAC
UAUUUAUAGUUGGUGAAGUCUUUCAUUAUUGAAUAGGAUGAACUGUGAGUAAUAAAGUUG
GUAAUAAAUAGGUUAUAGGUUACAUGAGUUACAAGGUGUAAUGACAAAAUAAAGAAUGAA
UAAUGAAUAAAAUGGUUACAAAAUUCAAUGGCAUGAAGUAGUCAAAGGCCAAGCAUUUAG
AAGGUAAAGGAAGCCAAGAAAUUCAUGAACAUUUUACCAAAUAAAGGUCACCUAAUACCU
AGAAUCAAUGGCACACAAUGACCACCAAAUAAAGACAUUUUCCAAUGUGCAUAUUGCCAC
UAAAUGUUGGCAGUAAAAGAAAAAGCUUUGACCAAGCAAUAAUGGCAUAUAAUAACUUUC
AAGCAUUUGAAGAAACGCUGCCAACAGCCAUGUAACGUGAGGAAUAAAGGAUUUGGAAUU
UUAUAAAAAGAAAUAAACUUUAAUAUAUUUAACAAUAUUAAAAUGCACCUUCAUGAGAGA
UACAAUAUAACAAAGUCCUCGUGGAUUUCCCAGGUUUAAGAUGCUUAUUGUGUGACUGGU
UGAUACCCAUUACUCCUGAGUCUUUAUGAAAAUUAAUAGGAGCCAGCAUCAGCGACAAAA
UGCAAUCCUAGCACUUCAGAUUUUUUACACUCGAUUGCAGUGCAUGAAGUAUUUAUCCAG
GUUUAAUUCUGCUACAUCAAUGCUGCAUCUCAGACUAUGCAAGUACUAAUGAACAGAGUA
ACCAAACAUAGUUUUCUGAUUUCUGUAUAUAAAAUUCAUGCUGCACGAUAAGAGGGAUGA
CAUAUACUGUUUACACCUAAGAGAGGAAAAAGGAAAACAAGCAGGGCAAGAGAUGUCUUA
CUGUCUGAAAUUUUAAAAAAGAAGGAUAAAUUAAAUGGGAUGCUGUGAUGCAACUGCCAG
UGGUUUUACCGGAACAGUUCUUUCUGUUGAAGAUCAUACAUGAUUUGUAUUGAUUUGAUU
UGAUAGCAGUAAUCUUACCUAGAUUACAUGUAAAUUUGGCAAAAACAUCUAAAUUACCAA
AACAAUAAUCUAAACCCACAGUAUAAAUGCCAAAACAAAUUUGAGGGAAUAACCAAACUU
AGCAAUUCUCUUAAUCUUUCUUUCGUCAUUCUUCAUAGCGCCUUUUUAGGAUACCGGAUA
AGACAAAGGCAAAAUUUCAUAAAUGACAUACUUAUAACUUUCAUCCGUCUUUUGAGUUUG
AAGUUGUAUUCGUGUGUUCCAAGUUGUGUUCGCGUGUUCCAUAUACAACAGGAAGUUGUA
UAUGGAAUGUCAGAUACUUUUUUUUGAGUUUGAAGUUGUAUUCAAGUGUUCCAUAUACAA
CUUCUAGUUGUAUAUGAAACUUAAUCCAUUUAUGCCAUUUUAUGUAAUUAUAUGAAACCU
GUUUUAUUAUAUGUAAUUAAAGGCAUAUGUGUGCUAGUUUAGGUAAUUUUUCCUAAGACA
AACUACUAAUUCCUAUAUCACAAUUCAGCCCUCCUUCUCUCCAAAUCUACUUGAAUUGCU
CUCAUACUCCUAUUAACACAAUUCUUCUAUAUUCUCUGGGUAUGAUCUACGUCUGGACAC
UGUGCUAGUGUGUUAGAUCUAGUACACGAGUAGAAUAUUGAUCUUUGGUCCUACUACAUG
UGACAUCAUCUUAUUAAAAUUACUUCUCCAAGAGCUAACGUGCAUUCAAUUAAAACAGAU
AAAGCUGAUGUGAUCCUACUAACGAUUAAGUUGUCCCUCAUAUUGCCUCAAUUAAUUGAC
UAAAUUCAGAAGGAAGCAAGUGAACUGCUUGAUCAAUUCAAG

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 [-498.66] kcal/mol.

2. The frequency of mfe structure in ensemble 1.97042e-28.

3. The ensemble diversity 646.02.

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