lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-388.70) is given below.

1. Sequence-
AAAAAAAAUAUAUAUGCGGAAGACAACCCAAAAACGUGAUGUCAACGUCGAACGAACCAU
AUAUACAAAAGAGUAGCCAAAAGAGGAUAUAUACAAUAAUCAAAAUAAUCUCCGAAAUAC
AAUGGAGACAAAACCAAAAUACAAUAUACAAGAGGAGAGUCAGGCUGGAACUGCACGCCA
AGCUCACCCUGAAGUCUCGAAGUCGGAGAAAAUGAACGAUCGGCGCUCACGGUCGAGGAU
GAGGAGAACGAGCGUAUUCUCAUCGGAGCGAAUACGCUCGGUCACUCCGUGUCAUGAAUG
CACAAUCAUAUCAUACUAUGCAAACAAGUCUCAAUAAUGGCAUGCUUUUAUCACAACCUA
GGCCUCACACCGGCCACCAAGUCCCGGUCCCGUAUUACACAGGUACCAUCGGUAUAACAA
CCAUAAUAACGACAAUUAAAUGGACGGAAGAAAGACACAGAUAUCGAAUAGACCUAACUA
CCCCUCCCAAGGAAGAUAUUUAGUACAAUUAGUUAGGUUGUGAACCCGGAGUUAGCCCAC
AAAAACCUACCUGUCGUCCGAUGAUUAAGCUUUUGCGAACUUCACGGAGAUUAUUCCCCC
UUAAUCCAAACGACCUCCGAUCAACCUGAAACUUGCGCCAAAGCAUUCUAAACGGCAAUA
CGAAUCCAACGGUGCAAUUUAAAUUGAAUUCCGGAUCGGGUCCAAAAUCGGACCUAAAAC
GGGCUUUACGGGGCCCGCUUGCCGAAAUCAAAAACUAACUUCACCACUGGGUUUCCAAUA
CCAUUAGAAACCCAUGCUCCAAAAUUGAGCUUAAGGCGAGCGAGAAUUGAUCUCUAAAUC
AGCUCAAAACGGAAUAACCCCUAAAGGGUCCAAAGAAUCGAUAAAACGAACAAAGACUUG
AAUAAACGAAGAAUUUAUGAUUCUAAUAGCAAUAUAAACUAUUACUAAUAAGAAUCAAGC
CAAAGAAACCGAGCUACGAUGGUAAUACAACAACCCUAGCUCAAGGUCAUCAAUAGAGGA
AUAAAGAAAUAGAGAAGAAGAAGAAGAAAGAGAAAGAGAACUUACCAACUACGCAACGAC
GAAGAUGGCCACGAAAAAUUUGAUCUUGAACCUUGGAGAUGAAGUUUGAGAGGAAACCUA
GACUUGAGAGAAAAUGAGGAGGUUUGAGAAUAGAGGAAAUGAAAGAAAUGAGCAAAAGGG
CUGAUUUUUAAAGAAAAAAACACUGGCUGCCAGCUGCUGUUUUUUUCACUGUUUUGGCUG
AAAAUUUCAGCAACAUCAUCGCCACCUCGGGGAUCAAACGGAAGUCAAUUUUGACGAACC
AAAUAUGCAAACACAUUGGAAAUGGCAUUCCGGACGCAAUGGAAUCGACGAAACUGAAUU
CCGAGGUCGUUUGCUCAAAAUGACCCCCGAAACCAAAAGGAGCAUUUCUCUAACGACACC
UCAAAAUUACAACGGAAAUCCCAAAAAUUACGACACCUCACCUAGCCUAAUUUCAACAUU
CCGGAGCUGCUGGAAGCGUCAGAAUUCCAUUCCGACACUCCGAACAUCGAAAACCAACAA
AGCUCCACUUUUAGGCUAAAACUUAAACAAUUUUCACAAUUUCACAUAACUUACGAACGG
AACUUCAAAAACACAAACUCAAAGUCAAUCUUGACUUUGUUUGGCCUUCCGGAGCUAACA
GAACCGUCGGAAUUUAAUUCCGA

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 [-416.91] kcal/mol.

2. The frequency of mfe structure in ensemble 1.31322e-20.

3. The ensemble diversity 359.96.

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