lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-332.20) is given below.

1. Sequence-
GUGGGAAGUCAUAAAUACAGAAUGGGAAAGUUAAAAUGUACUCACAAAGAUUUGAUCUGC
AACAUUAUAACACAGAGAUAAAAGGAGUUCACAUCAAAGAGAUGAGAAAGAAGGGCUGCU
AAAAUCAUUUCCCAGUAUUUCCCACUGAAGUUGAAACAUUUACCGCUAACUUCAAGUUCA
CUUCAAUCGCUUUGCCAGCUACAAUUUUGAGGGACACUUGAAUACAGACCUCGUAUUCAA
CUUAAUCCCAGAUCAUAACUACGGUAAGUAAACGUAACAGUACUGCAGCUAACAGCGCUU
UUCAACAAGGCAAAGCCAUCACUUUUGAACAAAAAUUACAAAGUCUAGGGAAGAUAUAUA
GUAUAGAAAAUACUAAUUCUUCGGUUACUUUCUCGAGGCGUUCCUCAGAGUCCAGGAUUU
GCAAGGAGUAGACACAUCACAGACGUAGCAAUAACACUGCACCAAAACCCAAAGGCACAC
AAGAUUAUUAAACUAAUACUACAACUACUACUAUAUAAGACAAAGCUUGUGAGGCAUUAA
AAUGCAUUACGUAAGUAAAGCUGAAGUAAUCUCAUAAGGAAAAUGUAUAACACCAAAGUG
UUUCAUGUUUGUAGAGACUCAUUACGACAACAAACAUACCUAAUAUAAUCUUACAAGUGG
GGUUUGAAAGGGUAAGAUGUACACAGAUCUAAACAGAACAUGUUGCAAGAAAAUAUGGCA
GUACCCUAGCAAUAUACAAAGCAACUAAAACAGGAAAUCAAGAAAGACUAUGCAGGAAGA
UGGACACAGCCAAAAAUAACGUGUAACAAUAAAUGAAGUAGAAGAUUCUAUAAACUAAUU
UAAUAGACUAAUCUCAUAAGAUCCCCUUUUUGUGUCUGUAUUUAUGGAGCUAACAAUGGA
UUGUAUAUAAAUACAGAUAUCAACUGUACAGGGGUUAAUUUCCACCUAGACAAGAAAGUU
UUUAUUGUUGGAUCAUAAACUUGAUCCAUUAUGAGAGCCCAAUAAAAUUGAAGCCCAAGU
CCACAAUCAAGGUCCAAGCCUUCUACCUAGAAUCUUCUAGGAUGUGGUAAUUGUGCAUGU
GAAUCAUUUGGUAACUUAAAAUAUUAUUAGAAGGUUGGAGAAGAAUGAGGUGUAUGGUUG
UGAUAAUUUUGGAUUAAUUUAUUUGUAUGGUGUAGAUUUGCUUGUUAGUAGUAUAAAUAC
CCCUCCCCAUUUUGGUUUAGGCAUCAAGAAAAAUUAAGAGUUUCUAAGUGAGUGAAGAAG
UAGUCCAAUAAGAGUGAGUUGUAGUAUUUUGUUUUUGAGUGAGAGUGCUCUUGUAAUAUU
UCUUUGGGUUUGAAUAAAAGUUGUUUGUGUGAGUGUUUCAUUUCCAACAAUUUGUUUUCC
AUCGCUGAUAAACACGUAAAUUUCAGAAUUUUCUUUAGCCUUUUCUCUUUGAAAUCUCGG
UACUCCAUGUUGCUCGCUCAUUCAGCUACCGUCCCUCAAUGUCCUUAAUCAGUAAGCGUU
CGUGUCCAAUUUGGUUUCUUCAGUAUUUCUUGCACUUGCU

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 [-360.27] kcal/mol.

2. The frequency of mfe structure in ensemble 1.6484e-20.

3. The ensemble diversity 365.65.

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