lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-358.00) is given below.

1. Sequence-
GUUCCCGUUCCCGGUCUCGCUCUUAUACUCCUUCAGGCUCGUCUUCUCCUUCUCGUUCCC
GUUCCCGGUCUCGCUCUUAUACUCCUUCAGACUCUCGCUCCUCUAGUUCGCGUUCUCCUU
CUCGAUCUAGAUCCCGCUCCAGAUCAAUUUCUUCAUCUUCCUCUGCUUCCCGAAGUGCUA
GUUCUCGUAGCCCCAUCCCCCGACGACCUCCUCAGAAACGAAGUUCUAUACAUAAUGCAC
UUUGUAUAGUCAUUUUUCGCCUUUGUAUUUUCACGUCGAUUGUUUACUGGAAGAACACGU
CUAGUGUCGGAGAAUUGAGCUGAAAACCUAUAUAGUACCGAAUGAAACGGAACAAAAUGU
ACUAGUAAUAAUUCAUAUUAUCACCUCAACUUCUUUGAAUUGAGGUGCUGUUGUUGGUUA
AUGGCACAUGGCUGCUCCAAUUAUGUGUUUAUGAUAGAUUUUUUUUGGAUUGUUCUGCUU
CUAUGUUCUUUUACCAUGUUCAAAGUUCAAUCACGUUGCUGAUUCAGUAGGAGUGUUUGG
UUAUUGCAUCUUUAGAUAUCUUAGCUGGUUAAUUUGAAAUCAGUAGAUAGUAACCAUUAU
UGUGCUGAGAGUAAGAAUGAACUCACCUUAUAAUUGCUAGUUUCUUUCAUUGUUAGUGAA
UCUGAGUUCUGAUUCUUGGCUGGUUACAUAGAGAAUGGAUAGAGAUACUCUCUCUUGCAU
UCCAAUUAUUAUUUAGGAUGAGAGGCUCAUUUGAGGCUUAUAGUUGUGCUCUGUGGUUAU
AAUUCCUAGUUGUUCCAUAGUGUUCCCACGGCUGAAGAAUAUUAAGCUGUGUCUUCUAUG
UUAUGGCUUUUCCCAACAUGCAAGUAACAAAACUAGACAUUGGUUGCAUCUAUUUUUAUU
UUCUUGCUUUUCUUUAGACAACUACAAACUAAUUUCAAAUAACUGUAUAAAAUAGUGUUG
GGAACAACACCCAAGGGUGUGGCAUACCGGUCAAUGAAGUGGGUGAAACUAUGGAGACCA
AGGUUCAAAUUCAGCAGAGGCAAAAUGCGCUAGGUUGUUUCUACCCAUUUAAGCAGGAUG
UCUAAGCAUUUAUAGGCAGAAUUAUCCGAUACAUGUGUUGGUAGGGUAGCAAAUACUUGU
UUGUGGAAUACUCGAGGUGGGUGCAAGCUGGUGCCGACACUUCUAGAAUUUAAAAAAAAA
AAACUGGAAAUGGUUAGUCUUGAAAAUUGGCCUUGUGUUUGUCAUCAUAUAUUUUUGUUU
AUUUAUUAUUGAGCUUAGUCAGAUUGAACUAGCAUGAUAGUUUCUUGUUAUGCUGUUAUA
GUGGUUUCCCUUUCUGAAAAAAUAGCUGAGGCUUCCAGUCUUCUUAUUGCUGGAUGAUCC
UAAACAUAUCAUUUGUUGUUAAUAUGGUUUUGUUAGCCCUGGUGGAGCAUCUAAGCGUGG
CCGCUCGCCACCAUCAGAGUCUAAGAAAGCUUCUCCACCUCCAAGG

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 [-384.45] kcal/mol.

2. The frequency of mfe structure in ensemble 2.30984e-19.

3. The ensemble diversity 485.29.

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