lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-328.74) is given below.

1. Sequence-
CCUUCAGACAUUAAUGCCACAGGCUCCAUUCUCUAAUUAUUACAACUAGAGAUUGAAAGA
AAUAUAUGAGGAGCUCAGAUAGAAGCACAUAUUUAUACCUGUGCAAAUGUAGGAAGGCGG
AGUAGAUUGACUUUUGUAGGUAUAUCAAUAUUCUAGGACUCGGCAACCAAUAACAUUUAA
UAAACAGAAUACGUCCCGAAAGUUUUAAAUAUAAAUAUAUUUUGUCUAAAAAGGGCCAAG
UACAACUAAGAUAGACUUAGUUCAACCAGAUACGGACUAAAUUAUGCAACCCCAGAGGGC
AUUAAAAACUCGACAUUUAUAAUUAGUUCUCUGAUAAUGGCUAGAGUAUAUACCAAUCAU
UGAGAAAAGGAUCAAGUAUUAUCAGUUACUAUCAACUGUCCAAACUUUAUAAUUAGGAAA
AUGUAGAAGUGAUAUGGGGAAGGAGAUUGAGAAUCAAAUGUGGGGGUCUUUUUCAAUACA
UUAAAAGGCAAUAUAAAGUAAAACCACUAAUGGCAUCAGCUGAGAAUAUGCAGAUUGUGG
UGGUGAGUUUGACAUUUUUAUAAGGGAGAGAAUUGUAAUCUAUCUUUCAACUCCAAUACU
UUAACAAAGUCGAGAUAUGUGCAAACUGAACUAUUGACUAUUGUUAGUCCCUCUGUUGGU
AGUUGCUCAAGUAUUAGACUCGUCCUCACCAAACAUAUCACCUAUGUCCUUAUUUUCUAA
UACCUUGAUUCAUUUGCUUUCAAUCACCCUUCUUCCUAUAUUUCCUACUUCUUCCUCUAU
UUUUUAUUUAUCUUAUUCUCACACUAUGAACUCGACUGCCCUUUACCUAAAUGACUCCAA
AUCUCUCCUACUUCCUGGAUUCAAUCGACUGAUGAUGAGACUAUUAGUCGAUUACUCCCU
GGAUCCAGUCGACUGAUGACGAGACAACUUCAUAUAAUUAUUAGUCUUUUGAUUUAAGUA
AUUGUAAACCACAAUAAAUAUUGAGGGUGAAAAAUGUAAUAUGAGAGUAUAAAAUAAACG
AUUUCAUAAUUUUUAUAUUGGUUUUGAACCAAUAUGGUAUCCUAAUUCUGCUUCAUUAGG
UUGCAGGGAAGUUAUCUCUUUUAGCUUUUUGUAACUUGAGUUUGAGUAUAGUCUUAGUGA
UUUUCAGCAUUCACCACCAAUUUCUACUAGGUUGGAUUUCACUCGCUCACUAACAACGAA
CAAGAGAUGGUUUUGACACGCUCACCAACAAUGUACAAGGAUGAUUUUUACUCACUUAAC
AAUAACGAAUCUUUGAUUUUCACUCGCUCAUAAAGAAACGAAUAAUGACGCAACCUCUCA
AUACAAUGCCUCACCAAAUAAUAUUUUUUAUCUCUUCUUUCUUUUGACUACACAGUAAAU
CGACACUGGAUUACAGCUGAAAUAUAUCUAGCUCCCAACUACUUCACCUGAGAACCAGGU
UCUUAAGAAGAUUUCAGUAAAACUGCAAAGUAAAGAAUACACAAUUUUACGUAGAAAAAC
UCCUAACUUUAGGAGUAAAA

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 [-352.77] kcal/mol.

2. The frequency of mfe structure in ensemble 1.16358e-17.

3. The ensemble diversity 276.93.

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