lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-521.30) is given below.

1. Sequence-
UUUUAAACCAAGUCUUGAAAAUCAUUUGUAACUAACAAAUAAACUUACAGGAAAAGUAGC
ACUUUAAAGUCAAGUAAAAGAGAUGGCAAAUCUUGGCUGGGUGGCUUGGGGGACCAGCCA
AGAAACUUAGACCUGCUUCUCCUUAUCUGUAGGCCUGAGAGAAAACUGAACCCGAUACUU
GUAGGUUUUGACAUAUUUCGCAACAACCUGUCCUAAUUCUAGCAAAGUGGGCCUUAUGUC
CCAUUACAAACAGAAUAAAACAAAUAAAUAGGUAAAUAAAAUGGGCUUCUUAUCCCCAAA
AAUGUUAGCUGCAUGUUGCUUCAUUCAAAUGGGUUUCAGCCCAUUUUGUUCUCUGUUGGA
CUACUAUUACAAAAAUAAUGGGCUUGGGCCCAUUAUCAUUUUGCUGUCAUUGGCCCAAAG
AGACUUGACAUGGUUUGGACUCAAAAUGCAAGAAGAGAUAAGUCCAUAUUUGACUCGGAC
UAGGAGAUUUUCAUGCAUAGAAAGAAAAGGAAAAGAUUAGUCUAUACUUGAGGCAUACAA
UAGAGAUGUAGAUGACAUAUUAAAUCAAUCAGAACCUAAAGAUAUCCAACUAUACAUGGA
CAUACUGCUGUAUACUAGUAUAAGCUCUUAACAAGUGCCCCAUUUUUAAACCUUAAAAAG
AAAGAUGCUCAAUCUAUGAAAGACAAGGUUGGUUAUCGUACACCCAUUUUCACAUAAAUU
ACAUGCUUUCUAAACAAAUUCAGGUCACAAGCACCAACUACAAUUACUGAUUUAACAAAC
CUUCACUAAAAUUAGUACCAAAAUAAAUAAACAGGGCCAAAACUCCUCAAAGGUGAGGCC
UUUAUCAGUUAAAGAGAACAUUAUUUGAGCUAUUACUUAAUUAAAUCAGCACAAACUGAA
AUUAUACAAGAUCACAUAUUAUAUCAUAAGACCUCCUAAUCCUCUAAUCAAGGUCACUCC
AAGUCUAAACAACAGUAAUCGACAAACCAACACAAAAAUCAACAAAUUCACUUUAAAGAC
GUCUUUAAUAUCAAACAAAGAUUACACUAGUUAAAUCUCAUACAUGCUAUUAGAAGUCAA
GAAAGUCACUCCUAUCAUUUGACUUUACUACAUGUUGAUUCUGUCUUUUAAACUCUCAAC
ACAUAAUACAUGAAUCAUUCUUCUAAAAUCAAACCUACAAGUGAACUAGGAAUAGAUCCC
GAUAGACCCUAAAGCCUUACCAAGGACCAGAUAAAAACACCUCUUUCACUUUAUUUUAUU
AAACAUACUAAAACUCAAACACAUUUUAAACAAAGACUCCAGUUUUAGCAAGAACAAAUU
CAGCAGAAAACUUGGAUCUUAAUCCAUAAUUAGACUUUCUUAGUCAUAUCACAGUCUUAA
GAUCAUUUUCACGUGAUUUCCACUCAGUAAGCAGGAGUCACACAGAAAGAAAAAUAGAAA
CCUAGCACAAAAUCCAUAAGAAAUAGAGUAAACAUCAACUCAAAAAAUAAAGUAAGCUAU
UACUCACUCAACAAGCAUACUUAUUUUGGUAGCUAACUAGUAAGGAGGAUGAGAGAAAAG
UGAAUAUUUCACCUAUUUGGGGCAGGGAGUGGGAUAUAUAAAUAAGUUCAGAGGAUUUUG
ACAAGCUUUAGGCUGUGGAUUCUACUUGUUCGAUGUGAUUUUGUAUUCUAGGAUUGGAGA
GCUAAUAUUAUCUUAGAAUUUUAAGAGAGACCCAUGCAUACCCUUUGUUAAUGGGAUUUU
UGAUGGCUAGACUUGAAUAAACCUAGGCGCCUUUGAAAACCCCCAAACCCCUCAUUUAAC
UAAGAAUCCUAGCGUUUCUCUCUAAAAUGAGAUCAUAGCUUCCCCUAGAAUCCAUAAACU
UUAUGAACCCUAUAUCUUAUGACCAUAGAAUCCUUAGGCUUCUCUCAGACCCCUCUUUUU
GCGGCUAACCGUAAACUCUCUUUUAAAGACUGAUUUAUAUAGAUGAGGGGACCUAGGGUU
CAGGGGGAAACAAAAUGUGGGGAAAAGAGUGGAAUUCUAGAGGGAUAAGGGACAGAUGGC
ACGAAUCAGCCCUAUCACAGUACUGAGAUCAAAAUCAAAUUGACCAAUUUUGAAAUUUUA
AACCACUGCUAGAACUUGACCUAUCAAAGGUCAAUACUUACGUACAAAAUCAUACAAGGA
AACACGUUGUACAACUAGUUCUGAAGGGAAGAGAUGAUAAAUUAAGGAUUCUUACCGUUG
GGAUCGAAGUGAGAUAGCCUUCAUAUUGUAUUCGCUGAUAGUAAUGAACGGAGAGAAACU
AAAAACCCCUCUUCCUCAAAUGUUAUCUGAAGAACAAAAAACCAGAGUUGGUAGUCAUUU
GGAUGAGAUUUUGGAAAAGAAUCGAGGUUUCGUUGUUCUUGCGAGAAACUAAAAGAAAGA
GAGAGGUAUGAGAGAGAAGAGUCCAGCGGGG

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 [-564.38] kcal/mol.

2. The frequency of mfe structure in ensemble 4.38392e-31.

3. The ensemble diversity 574.58.

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