lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-535.40) is given below.

1. Sequence-
GCCUUUGCCCAAGGAAUUGUCCGCACGGCAACCAACUACGAAUGAGAGCCAAGAUUUAUA
AAAUACAGGCAACUGAGAGAAGAAAAAUAACUUUUUCCAUUUAACGAAUAUUUUCACUGU
CACGGCAAUGGUGUUACAGCACCAAAGCGUUAGAAAGAGAAGAUUAAAUAUCAAUAAAAG
AGGGGUCAGUUCCAUGAAGACAAGACGGUCAAACUUAUCAAGAGCAAGAUCAUUUGUACC
AUACAGUUAAGCUGAUAACCAAAGUAAAAUUGGUAUGCUGUGACGGUCUCAUUCCCCCAC
CCCAACCCCCCUUCACAAUUCUGGGAGUUCAUGGUUGAAAACGUUAUUCUCUUCACAUGA
GUUGCAGUCAGCACUAUCUAGCAACUUUUUGACCACCAAAGGACUACAGAUAAGUGGAAC
UUUUGACAAAUUAAUGAUCAAUAUGAUGUUCGAAUACAAUCAGAAUAGCAAGAGUAUAGU
CUCAAACUAAAAAUGCUUGGGUAUUUUUACCAACUUAUCUCUUCUUUUUUACUUAAACUU
UAGUAAAUAUUAGUGAAGAAACUAGUGCAAUUGAAAUGUUUUUCAGGUUUUAUACGUUUG
AGGAGAACUAGAAGAAACCAGUGGAAACAAGUCAAAAUGGAAACAACAUGAAGAAAAGGA
AAAUCUGCUCAGUUACUAGUUACUAACCUUCGCAGAGAGGAUUCACCCGAUCGUGGAAGG
UUAAGAAAUAAUACGAUGCAGCAAGGAAGGCUGGGAAACAUUGAUUGAAUACUUGCUAUU
UUAUGAAAGAGUUUUUUCCUAAUUUAAUGGAUCUUUCUUUUAUAUCAAGUAAGAAUAUAU
UAACAAAAAGGCAUUACUAGCCCGUUUACAAGAAGUAAACCAGAAAGUAGAAAAUCCUAC
GAAAAUAUAUGAUUUCUAUGAAAACCACCCAAUCAUAUACACCAAAUGUAACCUCAUGGA
UGCACAAAAAAGAAAUAAGGGAAAAGAGAGAGUAACCCUAGGACAUCCCCAUUUAGUCUU
AAUGAAAAAUCAAGAGAGGAAGUUGAGGUAGGGCUAGAUUAGUUUAACACGAUUUGGGAC
UUUAAACCUCAUUUAUCAUAUUUAACAUAGGAAUAGGAAGAAUCUAAGUGUAGCUUAAAG
UUGGAAUGUGCUAAAUGCUUCUUAGUUCGAUUCGAGAUAACAAGAUAAUAUAUAGUCUCG
CUAAUCUGUUGAGAAAUGAUUAAUGGGUAGGCAAAAGUCCAUUAGUUAUUGUGGAACACU
UUUGGGAAAUUAUAAUGACCCUUCCAGUCAUUUUUAUGUUAUCGCACUUUUCUUGUAUCU
UAGAGCUUUCCUGUAGUGGCCCUAAGUUAUUUAUGACUUGUUGGGACCAGUGGUUCAAUU
CCCGGAUUAUUUGCUAGGUUUAUGUUUGUUUCCCUAAUUUAGAGCCAUACCUUUUGAAAU
CGUUGACUUCAGCCAACAUUUUUUGAAAACGAACUCGAAAUCGAAUUUCGACAAUUCCGC
UAGCCCCGGAACGUGGAUUUUGUCUUAGAAGGACUCUUGAUUUGUGUCAGAAAACCUUCA
UUGUGAUUUUAUCUCAUUUUGCGUGUUUUAUGCGGUUUAGAGUUAGAAAGCUUGUCUUCA
GUCGACUUUCGAUGACGGAGCCUCGGAUUGCAAAUACGACUGUACCAUCCGCUCUGGAGU
GUCAAGUUUGGGUUAGGUGAGCUAUUGGUACAGAUCCCGAGCUAGUCGGGCUCAUUUUAA
GUUCUUGAGUGGAAUUUUAAAAAUUUAGGUCGAGGGUUGACUUUAGUCAACAUUUUGCCA
AAACAAUCUCGGAAAGAAAUGCCAUCUACGUCAUUGUUUCCGGAAUGUUGUUUUCAUGCA
AGCAACAUAGUUGGUUUGUGUUCAUCAGAUUUCGAGCAUCAUUUUCAAGUACGAUUUUGG
UUGGUUUCUGUGCUUUAGUUGUUGGUACAACAGACCAACCUUCAUUGUGAUCGCGAUGCU
UUGUCGUGUUCUCCUUCGCGACCGCGAGCAUCUGUCCCUUCAACCUCCGCAAUCGCGAUU
AUGAUGUUGCUUCAUCUCCUGCUUAGCGAUUGCGAUGGUUUUCCACCUAGUGCUUCGCGG
UCGUAAGCCUCAAGCCAAGCGAUCUCGUAGUACAAUAUUUGGCAGCCUAUAAAUACUUCA
AACCCCGAAUUUUCUUUCAUUUUUCCAACUUCU

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 [-574.38] kcal/mol.

2. The frequency of mfe structure in ensemble 3.42366e-28.

3. The ensemble diversity 685.71.

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