lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-462.74) is given below.

1. Sequence-
GUCAUUAAGAGUCAAAUCCAUGCUUCUCAAGUAGAGGUUAAAGGUAUCUACCCUUUUAAU
CUUGUUUUAUUGUAUUUUGUUCAUUAUGAGGAGAUCUGAUGUUUGUUUCCUUCAUUUUGC
UUACUUUCUAUUUGGUCUUUGUUUUUAAUCACAAUAAGUUAGGUGAAAAAUAGACCCUCU
AAGGUCAAAACUUGCACUCACAGCUUGUUUAAGGAUUCUUGGCUGGUCUAAUUUCUGUUU
UAUGAUAAAGUUAGAUUCUUCAGGUGAAAUGUGGAUCCUUUUGAGGAUUAAACCAAUGUG
CAAUAGCUGGCCAAAUAGGUGAACAACCUUUAAUGAAUGCUCUCAUGUUAAAAAUAGGGG
CCUUUAUGGUCUAUUCUGAGUUGUCUUGUACUUCACUGUGUGGUCAAUUUCCUGAUAAAG
UAUGUCAAGGAAUUGGUUUUGAAGUGAAAAAUUGGCUGCUGGUCUGAUUUCCUUAAGUUU
GGAUUUUUCAUUUGUUUAGGUAUGAGGUUCUAAAUUUGUUUGUCACAAGGAAAACUAAUA
AAAUUAUCUCACUUUAAUUGCUUUUAAGUUGUUGGUGAAACUCUUGAUUGUGAUUGUCUA
UUUGAAAACACAUAGGUCCUGUUGGAUAGAGUUUUAUCCCUGAUAAGAUGUGACCUUUUU
AUCUCUGAAACCUGUGGUUUGUGAAGCUUCCUUUUAAACGCUUGAAUGUCCAGUUAUGGA
UGGUUAAUAGGGAGGAUUGUAUGUUUCUCUUUCCUUUAAGUUUAGUUUAGUGACCCUUUA
GCCUUGAAUACGUAGCAGGUCCAUUGAGUAGAAAAGAGUUUUUGGCUGCAAGCUUAUCUG
UAAGUGUCAAGUUGAUGGCCUAUGAAACUCUUUGAGAACUGUAGCAUUUGUUCUCCUCUG
UUGCACCUUCAUUUACUAAAUGUCAAGCCUUUUUGUUGGUUUGCUUCUUAUAACUACUUG
UAGUUUUGGUGAUGGUGACUCAAAGUAAGAGAAGCUUCAAUUUGUAGGUUCUCCAAUAGC
AUGAUCUCUUCUUUGUGACCUCCUUUAUCCUUUGUCAGUCUCCUCUGUUUUAGAGCAUAA
GACCUUUCUUGAGGCUGCUCACAGUUGGUUCCUAGUUUUCUCUUGACGUCCCCUGUUUGU
UGUUUAAUACAUACAUGCUUAUAUGAGAUUUAAAGAACUAGUGUCUAAAGCUAAGUGACC
CAUUUCAGGCUAAUAUUGGCUUUCCAUAUGUUACUCAAACUCAGAAAUGGAUAGUUUGAU
AAGAAAUAAGAUGUUACCUAUUGAUACUUGACCAGGCAUGCUUAACGUCACAUUUUUCCU
UCCAUGGUUGAUUGUUUCUUAUUAUAUAGGGAUUUAUCUAUGAGAGUUUAACCAGCAGCA
UGCAUUAAAUUUUUGUUUUGUUUAAUCACUGAUUAUUUAGGAUAGAAACUGUCUGCAAAA
UCCAUGUUUGAGUUUCACAUUGCCUGCCUAAUUUAUGAUAUGCCUCCUUCACAGUAAAAG
UCUUAUAAUUUCAAUCUGUUUAGUACUAAUUUUUCUUCUUUUUUUUUAGCAUGAGUCUCU
CCUCUUCCAAGUCCAUUGGACUCAUUUUUAUCAUAUUUUCGAGUCAAGCCCCAUGCCAAG
CUCAAGUGGGAUGAAGAUAAGGAGUGAAGAAAGUUAAAUGGGUUGGAGCCCAUUACAUCA
GUUGGCAACAGCAGUAGUAUGGCCUAAAAUCCCCACAUUUUGUUUAUUAUUUGGUUUGUA
AUUGCCCAUAAGGCCCAAUUUUAUUUUAUCUUAUGUUAUGUUGAUGGUUGUGGGCUACAA
AGCCCACUUUAUUAUAUUAGGGUAGGUACAAGUUGCAAAUGGGCCAAAAUCCCAAGACUG
UAGAAUCAGGACAGGUUCUUGACUUGAUUUGGUCCAAAAGCCCAAGCUACUCUCUCUCCC
UCUUCUUUAUUUUUAUUACUUGUUGAGUGCUAAUUUAUUUAUUUGGACUAACACAAAAGU
AUUU

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 [-499.41] kcal/mol.

2. The frequency of mfe structure in ensemble 1.43769e-26.

3. The ensemble diversity 602.44.

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