lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-444.70) is given below.

1. Sequence-
CUAUAAACAAAGAUUUGACCAAAGGUUUCACAAACCAAGUCAAGAGAAAACAACACUAGG
GUGAUUAAUUCUAUCAAUGAUCCAUUAUAAUAACUAAAUACUAAAUUGAUUAUACAUGGG
UUUAAAGAUUAGCCUUUGAGUUCCAAUUAGCUACUCUCGAAUGCUAAUUAGAGUAUGUCA
CUAGCUUCUCUCGAAUGCUAGCAAACCUUCCUUCGCUUGUUCUCUCAAAUCAAGCUAAAG
CGUAUGCACAACAACUCAAUUUGGCUACAAUAGGAUUUUUACUAUCUCUAGUUCAAAUCC
AUUAAUGAAGAAACACUCUUUUAAUGCUAAAUCAAACUUUCCAAUCCUAACUAGCUUUCU
CAAGUCAAGCAAGGAUAAAUGGACAUUACCUAGGGUUAGCUACUUCCUUUGGCAUACCAU
AAACUCACAAUGGUUUAGCUCUAGCAAACCUAAAUACAAAUCAAUAACUAAAGAAUUUAU
AUAAAAGCAAUAGAUAAAACUAAAACCCAACAAUCUUGAAUAAAUAUGGAAAUAUCUCUA
UAUUCAAUAUUCAAACAAGAAAGAACAACUACACACUACAAAUAUUUAAUACAAAGCAAG
GGGAGAAGAAAUGGGUAAAAAAUACAUCAAUGGUGUCAUCCAAAUCUUCACCCCAAAAGU
GUAGUAGUGGUGUUGUGCCCUUUAUUGAGGUGUGAACAAGUCUAAGACCAAGUUUCCCUU
UUUCUUAUUUUGUGUGUCUCUAUAUCCAUCUCUCCCUAUAUCUUUCUGUUGUAUAUGAAG
AAAUGCUUUUUAUAAGCCUUAACUUUCUACCACGGCGGUCAGCUUAAGUGACUGUCGUCC
GGGACGACGGUCAUGCCGUGUGUCAUUGGCUAGCCGCCGUUCUUGGAAAUGGCCUCAACA
UUAUUGCCACGAGGGAUGGCGGUGAUCACCGUCAGGGGUGGCGGUCAGCCGUAUUCGGCG
GUAACCGCAUUAGGAACGGUGGUCCGCCGUCUUCGAUAGUAUCUUAUAGUAGCUCUUUGG
CCUUUAUUUCUUCUAAUUCAGCGUUUCAGCUUUCGUUCGCUUGGACAUUCCAAAAUAUAU
GCAUUCACCUGAAAUACUCACCAAACUAACGUCAGAAUUGGACAUAAAGAAGCAAAAGAC
ACAUAAUUUAACUAUUCAUUUGGAUGUAAUGAGUGGUGUUUUGGCCACUCAUCAGCAGCA
UCCUCCACAUUCGUUUGAGCUGCUGCAUCCUCCGCCAAAGAUAAACCUUCAAAUGCAUCC
UCGCAAAGGAGCAAGCUGCAUCCUCCAUCAAAGAAAAACCUUGAAAUGCAUCCCCCAUCA
AAAAACCUGGAGCCUCAUUCUCAUUUUUCGAAGGACCUUGAGAUUCACCUUCCUUUGAAC
CUUGAGAAUCUACAGGAGUGAUACCGCUCGAAUCAUUGAGAGUCGUCGAAAUAGUACAAU
GUGGGCACAUUGUUAUCUAGAAAAAAGGAAAAAAUAAUAGUUAAAUGGAUGCUUUACUCA
AAAUAAAUAAUUAAAUAAAAGUGUGUACCUCCAGAUUACUUACAUCAACGGGUUCAAUUG
ACUCAUUUUAUCAGGGUUCACUUUUCAGCAUCAUUUUUUUUAGACCGUACCUCUAGAAUA
AAGAAGGAUCAAGAGACCAUACUUUUGGCCGCAUGGACGGUAUUCGUUCAUAUACUAUUG
CCUUACACAGUAUUAAGGAAAUGACAAUGGUAUAUGAAAGAAUACCGUCCAUGUUGUGUA
AGGCAACAAAAUAUAAUAUACGAUGAAUAUAAUAUAAUAUAUGAUGAAU

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 [-474.58] kcal/mol.

2. The frequency of mfe structure in ensemble 8.77917e-22.

3. The ensemble diversity 391.58.

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