lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-403.57) is given below.

1. Sequence-
GUUAAAUUGUCAAUUUAUCAAACCACUAGCCAGUAUGCAUCUAACAUGUAUCACAAGGCA
ACAUACAUCUCAAGUCCACCAAAAGUGAUGAGUUCGAUAGUAAUUUUAUUUGAAAUUCAG
UUCCAUUUAGGAACUGAUUCAGAAAGGCAUGAGGAUUAGAAAGAACAGUUGAUGCUGUUG
CGAAGAAAUUGUUUGUUCCGUCUUCUUAUUUCUUAUCUCAUCCCAAAUUCUUCUGUCAAU
CCUUCUAAUUUCAGCAUCUCCAAACACAUCAUCAUUGAUAUACCAAGAACAUCAUAGCCC
AAGGCCAACUUGAAAUAACUCAAAUCAACAAGAACCUACUUUAUGAACUCUUGCUUUUUU
UUAGAGCACUGAGCCAGCAUAAGCAUUACUGCAGAGAUACAGUUGUCAUCUCAAAUAGAC
CCUAGAUGUAAACUGCAUGCUUUUGGAGAAUUUGGAGACAAUCACCCAUUGACAUUCUUG
AAAUUGGCCCUUGACUCAAGGAAGAAUAAGCCAAAGCAUCCAUAUCAUUGUCCACAAAAG
GACAAAAAUGUAGUGCUGUUAUUUAACUCACAAAAUGUAGGUACAAAAGAAGAAGCUGAU
GACAGCACUUACACUAUAUGAGUUUAUCAGACCCUACACCCAAGUUUAAAGGAGUAAGGG
UAUAGUGAACUCAAUUGUUUCAUCAUCAAGAAUUCAAACAAAAAUCUCAAUUGUCAAGAU
UUAGAACAAUCAUUAACGCCUCAACCGAAUCCAAUAUGAUCAUUUGUAAUGUAGCUUCAC
CAAGAGGUUCCCCCUGCUUAUGCAGGGACUUCGAUCCACUACACCUCAUAUUACAUGGAU
UGAAUCAUCAUCCGCAAACCAGACAACAGAGAAACCAAGCAAUCUUUACAAGUAAUUUAG
AAAUUGAAUAACAGAUAAAUGUAGCUGCUCUAGUGUACUCCAAAACAUAAUGAGAAAAGG
GGUUAUGAAGGAGAACUAUAAAAUAGAGCAACACACUUACUAUUGCUUCAAGGGAACGAG
UUUAUCAAAAAUGGAUUAUUUCUUGACAACCAGAUAAAGAAGCCUUCAAAUCACAACUUU
UACACGAUUAACCAGGUAAAAACAACAAAAAAGAUAGCAACUUGAGAUUAUUCAUAUCCA
AUUUUAACUAUAUAAUACUUCUUCCAUUAUAAAAAAGAAAAGCAGCCCUAUGCACUAAAC
UCCGCUAUGUGAGCUCACAACCAACACUAAACCCUUGUUAUCCAGCCGAUUCAUAUCAAA
UUCUAAUUGUAUAAUACAAUUUCACCAAAAAAAUUGGCAAUCCAAUGCACUACGCUAACG
CUAUGUGCAGGGCCUAAGAAGGGGCACAUAGCCAAAUAGGACUCCAAAAAGGCAACAAUA
AACCCUUGUGAUCUGGCUUAUUCAUAUCAAAUUCUAAUUGUAUAACAACCUCAUUAAAAA
AAUAGCCCGAUUGCAGGUCUGGGCACAACCACAAAGAACUCAAAAUAAACAACAAUAGGC
CCUUGUGAUCUAACACUCAUCAUUUGUAAAAUUGGAACAAGGAGAAAUUAAAAAGGCCUC
AGAACCUAAAGGUAAAUGCAACAUCAAUGGAGCUUAAUAAAGCCCCUCAUAUGGUACGGA
CAAUUACCAUGCAUCACCGGCCACAAAUAAACAUAAGUCAUUAUCCUUAACAAACACUAC
UUUCAACAAUUAACACAAAAAUCUAAGUUGCUCAAAACUCUCCAAAAGUGCACUGUUUUU
AGCAUAGGUAAAGACAACUAGUUUAGCGAAGUAGACAAAACAUUUUCUAGUAAAACAAAA
GCUAACUGUAAAAUAAAGUAUUCUAGGCUCAGACAAACGAACAGCUCUAUCAAUCACGGA
AUAUCAGAAGCAGAACUGGCAUUAAAGCUGUAAUUUAUAUCAUCACGGCCAACAUUUAAA
UAAAAAUAUAACACAAUUUUCACCAACAAACACAACAACAUACCAGUAAAUUCCCACAAA
GUGGUGGUCUGGAGAAGUAAAAUGUACACAGUCCAUAAAAAGUUGUUUCUGAUGAAAACU
CAACUGUCGACAAAAAUCAAACUCUAAUAAAACAACAAACAACAUAUAAUAACUGAAUAA
CAGCAAAUAGCACAACACUGUCACAAAAUAAUACAACUAUCUAUCCUAAACAACAAUACA
ACUCCAAUAAACUAGUAAAAUAUUAG

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 [-440.82] kcal/mol.

2. The frequency of mfe structure in ensemble 5.65979e-27.

3. The ensemble diversity 422.30.

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