lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-501.00) is given below.

1. Sequence-
UUUUUUUUUAAAUUACAGUGUGCGUCCUAUUUACCGUUUAUUCUUUUUUUGUUUAAAAAG
UUAACCUUAGUAUGUAGUUAGUUUUUUUUUUCUCUUUUUGGAGUGAAGGAAUGUUAGCUA
GUGUUAUCGUUAGAUAAACGUUUUGAAUUGACUUCAACUGAUAAUAAAGUCCUCUAAUUU
UUAGAAUACAUAUUUAGAUAUUUCAAUUCACCAAUCUGUUAAACUAAUACCACCUCUAUU
CUCCUUCAAAAUCCAAACAUUAUAGGGAAAAGACUUGAGACAGAGAUUUUCUUCCUGCAA
UAGGGUUACGUGUUCCUCAUGCACUCCUAAAUUGGAAUAAUAGUCUCGACUGUGGUGUUU
UUUCAUUUGUUGAAAAUCGAACCUAAUGGAGCAAAGAGUGGGAAUGACAGUGAAUGAGAA
GAAGUUCAUACAAUCUGCGUGAAAGUAGGAUGCUUAGUAUACCGGGCUGCUCUAUUUCUG
CUUUUCUGGAGUUCCUAUAUUUCUUGUUCUUUUUUUUCCUUUUGAUACGCGUGGUGUCCG
GGCCGACUUGUACACAUCUUGACUAAUUUCACGAGAUACCUCCCACCAACAAGUACCAGG
UAAUUCUGUCCACUAAGGCUAGAACAUAUGGGAAGAAAUCACCUAGUGUUUUGUCUCUAC
UGGGAGUUGAACUCGAGACCUCAUGGUGCUCAAUCCACUUCGUUGACCACUAGCCCACAC
CUUUGGAUGCUGCAUUUCUAGUUCUGCUGCAUUUACGUUUGGAUUAUCAGUUCACUUUUU
AGGAUAAUGUGGUGAAAGCUUGUUACAGAACUUACAAAUAUAUGGUGUUUGUGGUUUUAC
UGUGAAUCUUUUUUUGAUGAAGGAUAGUGGUGAAUUGAGGAAUUGGGUUUUAUUUGUUUU
UCUUUAAUGACUAAUGAUAGUGAGACAGAUGAAGAGAUGGAAUCUUUUUCUUACUAUACU
CAGCAAUUAUGUUGCAUAUUCUGAAUUGUUCAUGUUACUAGUGAUGAAAAGGAUGAAUUG
GCUGGCUUCUUCACAACAAAUUAUACAACAAUAGGAAAGGGAUAUAUCCCUUGAAAUCUC
CUCCAAUCAUGUUUAAAGCACGAUUUAAGUGGUUCAAGUUAUGUACCGACUUCAAAAAUC
UUUGAGGGAACCAUGGUGUUUUUGGCGAAGAUGACAUGUCUUGCACAUGAUUUUGAGGAU
UUUGUUAAUUUUGUAACCAUUAAUAACAGAAGGAUGUAACCUGCUCAUUUCAAUGAACUU
GAAGGGUGUUUUUUGCUUACAGUGAUAAGAUAUGAGUAUACUUUAAGGGAUGUUGUUUUG
CUUAUAGAAAUAUUUAAGGAUGUAUUUGAAGUUAUGAGUGUACUUCAGGGAUGCUUUUGG
CCAAAAACUCCUUACCUAUUUGAGUGAAAUCUUCCAAUUCUUCAUCUUUUCUGAUUUUCU
UUCUACUGAACUAAAUGGCGUUUAAAAGGUAUGAAAGUUUGAAUCCAGUCACUACAAGGU
AGUGUUUGCUCAUUACUCUUGUAUACGCCAAAACUUCAUGCUGCAGCUAGUUAUUUGGUU
AGAUAUUUGCUUAAUGAAACACAUUCAACCUACUACUUUCAUUUCUUCUCUCAGAUUGAA
AGUACUCUGCAUGGUACCAGAAAAUUUUGUGACUAAUUGCACAGUUGGAGCGGCUCAUGA
AGUUCCUGAUGCAAGCAGUCAACAUGAAUUGAAAUUAUCACCAUCGAUGUACAGUGGUGA
AUGGAGGAUUAAAGAAGGCUGUGUUUGGUAUUGGUCACCUAUUUUGAGUCCCAAUCACUU
GAUUCUGCAGCAGAACUAGUGGCGUUCUGAAAUAUUGAUUUGAACUUCUUUGUUGGACUU
GGGACUCCGGGAUUCAGAGGAAGACAAAAAAUGGUUUGUUCUUGAGAGUUUUUGCUGGCU
UUUCUUGAGCUUUUGAUGUUUUCUUUGUCCUUGUAGAGGAUUUCUAUUUAUAAUUGUAGA
GAAAAGACAAUCACAAUGUAGAGGAGAACUCUUCUGCUAGACUUUGACUAACCUACUAUU
UAUGUGACAACCCUAUUCGAUCAAGUUCAUAAC

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 [-540.47] kcal/mol.

2. The frequency of mfe structure in ensemble 1.53101e-28.

3. The ensemble diversity 525.50.

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