lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-600.90) is given below.

1. Sequence-
UUGAGCUUCCUUGGCCUGAACCAACUGCUUCGGUUUCAAGGUACUAUUGCAUUUCCAUGC
GCUCACUUUCUCCCUGUUGGCUAUCGCGAAUUGAAAGGUUCCCGAAAUAUGCGGGAGAUG
GAGUCCAAAGACUCCAGCAUUUUAUGCACACAAAAGAAAAAAGAUAAAUUAAUUAGUAAU
GAGACAAUUUAAAUACGACAUUCAAAUAGCAACAUAAAAAUUUUUAUCAUAUAAGAUACC
CGAUCAAUAAAUAUUAAUAAAGGGUCUAUUACGUUGUCUUGACCAUAUAGUCAGAUCACA
AGUAGAUUCAUAUAGUGAAACAAUUUCGAAACCACAACGCUAUCUAAUUUAUUAUUAUCU
UCAUGAAACGUUCGCAAGUUUCCUUAAGAAGAGCUUUGACGCAAUUUUUAGGCAAACGUG
AUGCCGAACUUGAGUAGCUAAGCUUACAACGAAAAGGGAGAGUAGACAAAAGCAAGAAGU
GAUAAACAAAUAGCUCGGUCAAUCCUUAGAAAAAGUAUUUUCAUAAUUCGAAUGGUCUUC
AUAUAUUCCCAUUUAAAGUUUUAAACACUAAAAUUUAACUUAACCAUACUCGAGCUUAAG
CUUAAUCAAAUAUAGCAAUGGUCUACACAAAUGAUUCACGUUGAGCUUUCAAAAGAUUUG
CUAAUUCAAACAAAUUCAAAUCUUUUUUUAAACUCAAAGAAAACAUAUGUUGUCCCAAAA
UGCAUGGCAUUUCAGGAAACGUGAAACUAACUAGAUUAGGAAAUUAAGUGCUCACCUUUG
AGUGAUUAUGCUAAAAAAAAUAAUUAACAGCUAAGUAAAUAAAAAGGCAAAUACUUUGAA
UAGUCAUAUCAUAUAAAUAGAGACUAGAAAUGUAAAAUUAGAAUAUUUCACGUGCAAGGU
UGGGAUAAAAUAAUUAUUCCAAAUUAUACAACUUAGUAUGGAACAGGCUGUUUUGAUGAA
CUGAUGCCAAACUCGUGUAGUCACAACAAUGGAACUUCAACUAUAUACAGUUCACCUGCU
CAGAUCCCGACAGGGUGAUGUUGGCGUAUACUUCACACACAGAAUUUGAAAAUGGCAUAA
UGACGGCCAUCAAUUCUUGAGAAAGAGAUGGUGUUUCGGCUAUAACUUUAGUCACAUAAG
AGAGGCGAUUAAUGAAACUUAAAAUAUGUCUUUAGGUUUCAAGACCAAUAGACCAACUCA
ACACUUCACAAAUUACUCAAAAAAGAAUCUCGAGUAAUGUCAUUAUGACAUUUAAUCUAU
AGAGUUCAAGAGUUUGCAAUAAACUCAUCCAAACCUCCAACCUUUACUAGAUGAAAUGAG
AAAUCCAAGAGGACUUAACAAGUCUUGAGGAUUCUCAAACUGAAACUUAAUAUUACUGGA
AUAAAUUUCCGCAAUAAAAAGGAAUUCCAGCCAGAAGUGCAGUAGGUAGCAACAAAUUUU
AACAAAUACAGGAAAUUAAAGUUUCAACAAAGACUAUUUCUUGAUCUGGGCAUUAUCUUA
UUUUGUCUUACAUAUUUUGAUACGUCAAUUCAAUAGAGAAAUAAUUUUCUGGACAUGAAC
UGAAUAAACAAAAAGCCAGAAAUCAAUGAAUCCAUAUAUGAAUUCACAUUUUAUCUUGAC
AAAAUAGUAUAUUUUCUUUUCAAGAAUUAUAUUUUCCUCGGCUGCUAUACAUACUAAUCC
UUAUGAAAAAAGGAGUUAAUUUCUUGAACUUUAAGUAAGCAAAAUACACAGAGAAGUGCA
GAGCUGAAAGUAAUUGACAAUAACGACAAUCACAAUAACAACGUGAUUAAUUACCACAUA
AUCAGCCAAACGAAAUUUGAAUAAGAACUGAAAAGAGAAACAUCAAUUAAAAGGAAAGAG
GAUUAUCACGUUCAAAUCUCCUAGCCAAGCUAACAGGAAAGAUGAUUUUUAAGAAAACUA
AUUUCUAGUUUUCUAGUCGAGGAAAGAAGAUUAUCAUGUUCAACGGAAAUUUAGAAAACC
AAUUUCUAGCUUUCUAGUUGAGAACACAUAGAGAUAAGUUAACAUAUGGUCACAGAUUGA
CAAAAUGAAAUCAUUUUCUCAAUAAAUUCACGGUAGUUAGGUUAUAUGAAGAAUAAAUUU
UGUUUGAUCAAAGGAAUCUACUCAUGCCUCCAGUAAAACUCGAAAUUAGACUAACAGGCC
CUAACAACACAGCAAAAAAUCAACUAAAUUUGCAGAAUUCAAAUAGAACUGUUGUUAUUC
UGCUUCAACUUUGAAAACAUUGUUGCGACAUCAGAUUACAGAGUAGAAAGGAAAAAACAA
GUUAAUUCUGCUUAUGAAAUCAGUUCACAUAGAUAAGCUAGCAAGGAAACGAGGGCAUAC
CAUAUCGAUUAUUACACAACUUCUAUCAAAAUAGAAAAUUUUCCAGGCCAUAAUUUCAUU
CACAUAUAACAUUACUCAAAACAAAUCGAAUAUGAGGCGAAGAUGUCCAACGCAAAUAAG
GCAUCAAAGUAGCCAUCGAAAACAAAGAAACUAUACAAUCAUUAAAAUAGAAUUGGGAAG
AGUAGGUUACCUUUUUCAGGGCAGUGAACUGAGACGACGACUUGACGAAAAUCGAUUCAC
CAACUUCACUCGAUACAGCAAAACAUAAGAAAAAAAAAACGAGACAAGAGUUCAUCCGAA
UAGAUAAAGAGUACGAAAACUCAAAUGAUUCCCCAAUUCUCCGUGUUUUGGCUCGACGUA
UGCUUCCUUUUAUAGGAGAAAAUGGAGCACCCAAUUUCAGAGUAGAGUAGGGGGGAGAUG
CAAAAUCAUGAAAAAAAAUUGACAAAACGGAUGGGGGAUUGUCAUAUUUUCAAACUGAUU
UGAGAAAAAAGGCAGAUACAUUAAUGACAAAAUUCUUAUCCUUAGAUUUUCUCCUCUUUU
CAAACGUAUUAGUGGAUAGGGGAGACUUUUGCACCAGUAAAAUUCCUCAGAAAAGGAGAA
AA

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 [-651.67] kcal/mol.

2. The frequency of mfe structure in ensemble 1.68475e-36.

3. The ensemble diversity 617.05.

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