lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-478.40) is given below.

1. Sequence-
AUAUAACAAUAUUAAAAGUUAUAAAUAUGUUUAUUGUACGAAGUGAGAUGGUUCAAAGUG
AUUUUCAUGUCGAAAGUAAUAGGAAAUAUAGACAUGCCAAAGACAUCAGGAAAAAACAUA
AGCUCUUUUGGCAGUACCAGUUGCUCAGAGAACUAGAAAGAGGCGCACAAUGAACCAGAA
GGCCGGCCCAAAUUGAUCGUAAAUAAUGUCUUCGGACAGCAUAAGCUUUCUGAGAUCCAC
UUCCUGCUACAUCAUUGAGCAUGGAAGCAACGUCCUCAGUGGUCACAUCUCUAGAUCAAG
AGGAAUCCACUGUGAAUCUGAGCAAGAAAAAACCACUAUUAUUUUGUCAAUAUCAUUUAA
ACCACCUUUCUGUCGACAAAACAUUAAAGACGGAAGUUGGGGAUUGCAGCGGGUGAAAGU
AAAGAGAACCUAAUCCACUUGUAUUUGGGCCUUGUGGUACUGAUUUUGGACAUACAAAAC
UUGUAGCUUAGACAACAGGCUGCAGUGCAGAUAAGCAAUUUCGUAAGUUCAGAAAUUAUU
UCAUUAGGUACAAUUGUCUUCUAAUUUUGCAGUCCAUCAGCCAUAUUCCAUUGAACCAAC
UUCCUCUUCUGUGAAACAGGGAGUAGAUCCCAAAAACUUCAUAAUUACUUGAAUGCGUUC
ACAUUACUAGGAGAAAAACAUCAUUUGUGGAAAGUCAAGGCGCAUAAAUGCUGAGGGGCG
ACAACUUCAGAAAAGAAUCAUACCCCUACAUUACGUACAGCUUAGAUCAGCAAUACCAGU
AUUUUUUUUUAAUAGGAAUAGAAAUGUAGUGCAAUUUAAAAUAAUAGCAAAUUAGCAACU
GAUAAAAAAAACUCAAAGAUCCACAAACAUUAACAAACAGAACAGUACCUUGCCUUAACA
UCCUUCACAUAUCCAAUAGGUGCUGCAGUAACAAUUAAGCAUAGAAAAGAAUCGAGUCUU
AUUAGAACAAUCUAACGACCUUCAUCUGAAUUCCGUUUUUUCGAUUUUUGCCAUAGGAAG
GUUCCUCCUUUAGUGUCCUCACUGCAAGGAAAUACUUCAUUGUUAAAGAAAGGGGGAAAA
GAUUGCUUAGAAUUUAUAUGACAUGAAAGUUACUGAACGAGGAACGAACUUGAGAAAAAG
CGAACUGAACAUCUCGCACAGUAACUUAAGAUACUUCCCUACAAGCUUGACUUGGAAUAG
CUGCAAGCAAGAGUUUGUAGUUUCUUCAAUGCAGAGAAAUAUGUGAUACCUUUUAGUCAU
GUGUACUCCUUAACUCUUUUUUGAUAUAGUAUUACCUUUGACCAGUUAUUAUAGGUUAGA
UCACACAUUUUGACAAAAGUUAUUUUUGUAACAAAGAUUUAGUCCCACACUUGAUGCACC
AAAAAUCAAAUAAAUGACACAUGUAUCAUCAUGGAUAGUCCCAUCCACAAUCUCUUCAUU
UAACAUAAUACCCACAUAAGAUAUGUAAUACACUUUUGUUUUUUGCUCUAUAUGUAUAGU
UUUUUGUAUCACAUCCAUUGUGCUAGAGAAAUAAAAUUAACUUACCAUUGUUCAGAGAUA
UAGAACACAACUCCAUCACCGUCCAAAUGUUAAAUCUCACCAUAUCCUGUCCACCGCACA
AAAGAUGCCUAAAAGGCUAACUAUUUUUCCUUUUGCCACAAUUCUACAAUCAUGUAGGAC
ACUACUUCAAACAGCUCAAUAGAUCAUAGAUGCCUCAGGGUUCAUUCAUCUCAUCAUUAU
CUUGUUCUUUUAGUAGUGAAGAAAGAAGUGGCACAAAUAAAAUUGACAGUAGAAACCAAU
UCUCCAUCAAACAAUUUACUCGAGAGACAGAUCAAGAAAUAUCUACAAUUUGCUCCCAGA
AUUUUCAUGGUUAAUGUUCAUAUUUUAUCAUGUCUUUAAAGGUUGCACCUUCCAGGAUCU
ACUACUAUUUUCAACCCUGUUUCUCAAGCAGACCAAGUAAUGAAAUCUCACCAACAUUCA
UUAUUACUUGUUCAUCUACAUAAAAACAACAACAUUACCCACUAAAAUCCCACAAAUUUU
UAAUGGUCUGGGAAUGAUAGAGUUUGUGCAGUCCUUACUACUACCUCUUGGAAGUAGAGA
GGCUAUUGCCAAAGGACCUCGGCUCCAAAGAAAUAUUUUUGGCUAACAUGAAAAGUGAAA
UACAAGUAUCAAACACAGUAAAUUUAUGAUCUAGACAAAUAAAUCUUCAACCAUUCAUCA
UGCACCAUCCCCGUACCUUCCAUUUUGUUCUAUAAAUUUGUGCUUCAAUUUUGUUCACUC
UGCUGUAUUACAUUACGUAACAGAUCCUCUUCAUAGGUGCAAACAUUAAACAUUACGUAA
CAGAUCCUCUUCAUAGGUGCAAACA

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 [-519.46] kcal/mol.

2. The frequency of mfe structure in ensemble 1.1711e-29.

3. The ensemble diversity 736.52.

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