lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-368.90) is given below.

1. Sequence-
GUUAGGUAUUAAAAGGCCUGCACCUUUUUAUAGAAAGUGACAAGUUUGUUUACGUAUUAG
UUGUUGAGAAGAGAAAGGAAUUAGUCCUUUGCUUUAUGUGUAGACUAUUCUAAAACCAUU
UGAUGGAGAAGGUGAAGGGGAAAAAAGUAGGCUUGGUCAUACCUAACCAUAAAACACAAA
GGGUUACGGUUAUUUAGCUUUGAAUUGGAAUGAUAUUAUCUUUACCAGUGAGCACUUUUA
CCCCAUGUGAGAUUUCUAAAAAAGGAGUGGAGGAACUUCUUACCUAAGUUAGAGGUUUGA
GUCUUGAGUCGAGAAGAAUAGAGAGGCAGACCAUUAUCCUUAAGUUCCGAAGGCUGACCC
UUAUUCUAAAGGAUCGGCUUCAGAUAAAUUUUACUGAGAUAAAGUAAAAAGCUUUUAUUU
UUUUUUUAAAUAUUUGGAAAAAAUAAUCUGUAGGCACACGCUUCAAGACUCGGUGAAUGA
UGAACUUACCGUUCUAUCUUCCUUCUCUUUAUACACUAGUUUUGUGUUCUCAAUAGGAUU
AAACUUAUUAGGUACGUCUAAUUUACACAUUAUAUAUACUAUGCUUUUACCAGUGAAUCA
AAACCAAUUACAUCACUUCUUGGAUGUGCUACACGACUUUAUGUUGAAGUACAGCUGUAU
GAACUGAUUUUUCCAAGUUGGAUGUUGAGUGCUUUAUAGACCAGCUAGCCUAGUCUAUUU
CUUGACAAAUUCUUUGCCUCCACCUGCUCUGUAAUAGUAAUCAUGAUUGUCCAUCUUAUU
GUAUCUGCUUGACACAAAAUAUUUAAUUAUUUCAUGUCUCAACAAUUUCAUUUUCCUCUU
AUGAGUUGGCAACUAAGGCAGUCAAAGCCAUGACGGAGCUAAUAAUUUAAUGAAAAUUGU
AUGAAUUUUUUUUUCAGUUAUAUUAAAGGUAUUUAAAAUUAAAUAUAUAUUCAUAAUAUU
UAACCUUUAUACUUCAUAUAAUAUUUUGAUGAAGGGUUUACGUCUAACUAUCCUUCACUA
ACGGUGGCUCUGCCACUGAGUCAAAGUGACACCUCUUCGCCCGUAAAAAUGACACUGUUU
UUUAUGUACAUAUCCUAUGUGUAUACAUUGAUUUUUCUUAGCAAAAUUCUGGCUCCACCA
AUAUAUUCGAGUAUAACAUAGAUUUGUGUUUGAUCUGCAGGAAAGUUGAUGGAAGUAGCA
UGUAGUAUGUUGGGAUCAUUUUGUCAUUAAAACACAGUUUCAAACAUAUUUGAGGAAACA
ACUCAAGAUCAAGAGUUGUGCCUCUAAUAUGUAUGAAUUUGUAGGUAGAAGAGGAGAAAA
AAAAAGUACAAAAUUUUCUGAAUAAACUGGCAAAUUUUAAUAUUUUUUUUCUAGGAGGAC
CUUGUAAAAUUUAGGGAAGGAGAAAAAAAAUAUUCAGAAAAUGUCAAUUUCCCAAGGAAG
AGGAUGGGAUUUUUUUUUUUUUUUGGGUUUUGUUAUAAAUACUGUAAUUACUACAUAUCA
AUUUUUUAUUUGUAUUGAAAGUUUGUUGGUAUCAAGAAAUAUAGUCUUUGUUUUGUCCUU
UCAUAUAUUCACGG

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 [-396.73] kcal/mol.

2. The frequency of mfe structure in ensemble 2.44191e-20.

3. The ensemble diversity 329.68.

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