lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-513.50) is given below.

1. Sequence-
CCCCAAUGCCAGACUUCUACCAGCACCGCCCUUUGAAAAUAAGAUGAUCCACAAGGAAUU
UGGACAUCCAAACCCAUACAGUGCUUGGGACACAACUAGUCACACAAAAGAGACAAGGGU
UACUUGGUCUAGGAAGGCCAUUACAGACAGCUUCCUGUUCUCACAACCCACAAUCAAGUA
CAGACAGAACGAGCUAAGUACAAUAAACUAAGAGACUCACAUGUCCUCUGCAUAUCAAGC
AUCCUUCAGGUAACCUAAAAGACAUGCAAUACUUUAGCCUAAUUGUAAAACUAGAGUCUU
AUGAAGUGAAAUAUGAUGUGACCUAAGUAGAACCUCAAGCAUACAAAUACAGACAACUUU
CACACAUUUCAAACAAGCAAACAUGCAUUAGAUCCUAAAUUCCACUUUUAACAUGAGACA
CGAUAAUAAACAAGUGAGCCUAGGUCAUGAUGCUGCUAUCACUUACUAAUUUUGGCCUCU
AUGUUACCUUCUUCUUUUUCCAUGGUCCAAAAAGAUUAGCAACAUAAAAACAAGUUAUCC
ACAUAACAAACUUGAGUAGUCUAGGCAAAAAGGCUAGGUCUUUUAAAGGAAAUGGGCUGA
GCAUGAUACCAUUUUAGACUUAACAGGUUACCAUAAAAAAUGAUUUUUAUUCAUUAAGCU
UACCUACUUCAUUAUGAUACAUAAAUUUACAUAUAAGAUGAUAUCAAACAAACCAGACUA
CACCUAUAUAUUCAACCAAGCAAAACGUCUUGCUUUCUUUACCCAUCACCCACAAAGCAA
CAUUUCAUAUAACCAAAUCUGGACUAGGCAGGCCUUUAAACAGGUUCAUAGCACUGAAAU
UCCAUAACUUAACACAUGCUUAGACUCAACAAGGUUCUUAAAUAUGCUGAUGCACAAGAU
UUCAUACCCAAGUUAUCACCAAAACAGAUAUACAGGCUGGAUGCAUACACUAUUGAUAAC
AAAGAUCCAAUUUUGACAAAGGAAAGGAUUAAACAAAACAAGUUGAACAUGCAGAAUACA
UUCGAAGAAAACAAAAGCAUAUUUAAAACAUCUUAUUCAAGGUUCAAACUAGCAGGAAAC
AGGCAGCCCAGGUCUUAAAGGAUCAGAUUUUAAACUUAACACUCCACAAACAGUUGAGAU
UAACACUAUUACUACCUGCACCAUUUUAAAGAGGUUGAUAUUUAAAUCCCAAUCCAUGCA
UACUUGUUUAGAUUAUUUAGGGUGAUCAAAAGAAAGAAUUUCCAGCUUUUAACCAUUCAA
GAUAGUGACAAUGUGGUGCACAGCAAAUUCUAAAGGCAAUAUUUUAACUCUUCGAUGAAU
GACAACAAAACAAAAAAUUGAAUGUUGGUUAAACAUGCUAUAAAUAAUGAUUGUUAUCGA
CCUUGGGACAUAUUCUUAUGCAGAAGCAUGUCAACUAACCAUUUUAACUUAGUAGGUUAC
UAUACUGGUUUUGACAUCAUAAGGAUUAAUUUCACACCUGAAAUAGCAUACUUGUGCACC
UGAAACUGUGAUCAAUAUAUUCAACACACAUUUCAAACUUUUCUAUGUCAUCCUUCACUC
AAAUAUCAUGCAAAACAGGGACCAACAAAUGUAGCUUAAACAUGACUUGGUCUCACUACU
AUCACUUAAGAAAAGGGACAGAUUUGACCAGUUUGGGACAUGCCAUUUCAGUCAAAGGAA
ACACCACUUUACACAUAAAGAGGCCAUCAUUUUGGAGAAUUUUAAGAGACUCAAAACACC
AGGGAUCAUCAGGUUUUACAAUCCAGUAAUUGCAAAGCUAGUUGACUCAUAAGGUCCUAG
UUAAGAACAUGGAUUAUAGGCUAAGGCAUUCACCACUGAGGAUAGGCUACUACACUGCUU
UGAAGGCACUCAAUCCACCAAAUUUUAACCUACUUAAUAAUAGACAUAACUAGAAAACAC
CUCGGUACUGUGAGUGAGAUUCAAAACGAAAAGAUGCAUCCUUGAAUCUAUCAUUUAGUU
GAAUUAUGCAAGGUGACAAGAGAGGCAGUCCCUUAAGGUCAUUUAACAAUUUAUAGGGAA
CUCAAACAACUUAUCAAGCAAUCAAUUCAAACCACCAGGCUAUUUUAAGACAUGGCUCUA
UUAUGAAGAGUUACUCAAAUUUAAAUCAAAUUCACAAGUGCAGAAGUCAUGUUCUCCUUU
UAACAGAUAUGUUUACACCUUACUAUGUAUAUCUGUAUUCUCCUUACAGAACACCAUAAA
UAAAUCCUUUGAAUACUCCUUAAUCAAGCUUUUAAGUGACAAAGAUGGAAUCUUUACAUA
UUUAACAACAAAGGAAUUCACAUAGCAUGCUUUGAGCACAUAAGUUACAAAAAGAGCAAG
AAGAUGGCACUUAAUUGACCAAAUUCACUUUAAGCAUGCAAGAUUGUACCUCUAAACCAA
CACAUGACAACAACCAUCCACUUCUUCUUCACUAAACACUCAAGACCAUGUGUUUAGUGC
AGUAAAUAAACCUUAAAGAACUCUCAUUUUGAUCACAUUUUAGUCAGUAAGCAAGGAAAU
UUGACCUCAAACAUGAUACUCUACCAGUUUUAAAUACCAAGCAGCGGCAGUUCACCUUUA
ACCCUACGCAUCACACAUAAACAUGCAUCUUACACUCAAGGGCGUAGAAGCUAGAAGAAA
ACUGAGGAUCAAAAGGUCUCAAACCAUCUUAUACAACAUCCUCUUACUCAUUUAAACACA
UAAAUGAUCAAAUAACAACAUUUUUGGCCCUAACAUGCUUCAUUAACUCCGUUAACCGUA
AAAUCAUGCAAGCAAUCUCACAAAACCAACACAUAGUUUAUAAAAAAUUAGUAAGAAUAA
UAAGAAAUUUAACAAUUUUC

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 [-565.05] kcal/mol.

2. The frequency of mfe structure in ensemble 4.74306e-37.

3. The ensemble diversity 669.09.

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