lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-394.10) is given below.

1. Sequence-
AAUUCUUUAGCCAAAAUUGAAGAUAAUCUUCCAUUUUAAACUACCCAAAACCUAAUCCCU
AGUCAGUUAAUGUUUCCUCCCUCCAAGCCGCCACCUCUUCAUCUUCUCUUUCAUCCUUCA
CUUCCUGUCUCUCUCUCUCCAUGGCCAAAAUGCGAAACCCUACCAGCCUUAUUUCAGCCU
UUUCUUUUUCUCAUCAUCCCCUUGGUAAAGCCUCAUCUUCUCGGAUUGGCUAUGUCUGGC
GAACCACCACCAGAAGCUUCAACCAAAUCUCAAUCUGCCGCUUCUUGCCGUCUCAUUGUG
CCUAUGCUUCCUGUUACUUGUUCGAUCAACAUAACUAAGUGACUUUUUUGCAAAUCUAAA
GGUUAUGCAAAUCAAAUGCCAUAGAGAUUACAAGGUUUUUUCUUAUUUGCUGCAUGUUUU
UCUCUUCUCAAAGAAUUUAAAUAUGUUUUUUUAUGCGUCUUCUCAGUACCAAUAUCUUGA
CCAUUGUUUGUUCUCGGGAUUUGGUGUGUACAUAUUUGAUGAUUUUGUAUAUAACCUUCU
GCCCUACAAGUGUUUGAUAAAAUUAUUGUGUCGAUAUUUCUUUUAAUUCAUCUGUAUUUU
ACUAGUGUCUCAAUUCAUUUUUGGUGUCUUUUUUCAUUUUUCUUUUUUUUUUUACGUGUA
UAUGAUGCAUUAUUUGCCAUACUGGCUCAAAAUUUUGCUUUAUGAGAAACCACAGUGAAA
CAUGGUGAUAUUUGACUCGCAAACAUGCAUGUGGAUGCAACCUUUUCUGAUUGUUGCUUC
UACUGCUUUUGAAUUUGGAUGAUUUUUGUGGUACAUGUGAUGAUAAACAACGAAAGUUAU
ACUUGUAUGAUAUCGAGAGUUCAUACCUUUUUCUAAAAGAAAAAGGUUGGACAGACAUCA
AAAUAUGCUAACAGCUAACAUACUAAGAUGUACUGCAGACAUUUUGAAUUUCAGCACUUU
UUGGGUGAAAUUCUUUUAUAUACUAGCCUGUUGAUGUAAUUUGGUCUAAAAUGCCUAAUU
GACACUAGUUUAACCCUAGAUAUUAAACUCGAACACUGCUCUACGUUUCUAGAUUGGUUU
CAUUAUUGUCGUUGAUAAUAUUUUCUUAGUCAGAUGAAAUGUAUAUUUAGUUCUUUAUGU
UGUCAGAUUAUCACAAAAUUACAAAUAGAACCGUCCCUGAUAAGUUUUAGCAGAUGUACA
AAGGCCGUUGAGGCAUUUUUGUUUGAAACUAAGUAGUUUCUAUAAUUGUUGAGCUGCUUU
UCUCAUUCUCUGUAGGUGCAUCUCAUUCUGCCGCAAUUACAUAUUUUAAAAUAAAGCACU
AUAUUUUGAAUACAUACAAAUUUUAUUAUUUUCUUGCCAAUUACCUACAGGAAGACCAAA
UGAAAGACAUUGUGUAUGGAGAUGACAUUUCCCAUUAUCAAGAUUUCAUGAAGUUUUACC
AGACCUACUGCAAAGGUAAGCAAGCAUAUCUUAAACAUCAAAUCAUUAUUAUUGUAUCCU
UACGUUCGACCUUUCCUGAUGAAAAUUACAAGUUUUUUCUUGCGAAUUUCCUAUCAUUAU
UAUGUGAUGUUUGCAUUGUACCUGAAAUAUAAAUAAAAAAUAUUCAGUAUUGGUAACUUC
AAUGUGCACAAACAUUCCAUCAUCUUUACUUCCCAUAUCACCUAAUAAUUGAAUGUGUGA
ACUCCUAUUUGCAGAAAAAAGAAACUUAUUCAGUUUUUGCUUUGUACAUAAAUGCGCCAA
UUACCUGAUGUAAUCAUGAUCGAAGGUAAAUAAUUUUUUUGUGAACAUUAAGUUCUUACU
AUUACUGAUUCACACUAGUUUGUGAAAAUGCUUUUUGGGACUUUUGUGGUUGUAAUUUAU
GUCUUUUUUUGAAGUUUAUGUUUGUGGGGUGAUGAUAGUCUUGUUAUUAUGACCAUAUUA
AGGUUGGACCUUUGUAUCAUUGAAUUCUAGGUUUCUUUCUUUUCCUUAGAUUUAGGAACU
UCUACUAUGGUAUUUUUCUUGGUUU

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 [-432.28] kcal/mol.

2. The frequency of mfe structure in ensemble 1.25493e-27.

3. The ensemble diversity 441.66.

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