lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-435.80) is given below.

1. Sequence-
CUUGUUAGCAACUGGGAGAUCUUUCACCCCAAGGUCACCCAAACUCUUUGGAGUUGUAAC
CGUCUCUCAAUUACCCAGUGGGACUUCCUUGUCCCGUCUAUCGAGUUCUGUGAAAAGUUC
CUUUGUAGUCUAUCCAAUUUAGCUGUGCCUGUUACACUGGUAAGUACUUGUAACAAAGGC
AAAGUAUGUGGGUCUAUAUAGGUUAGAGGAAAGCGUAGCACCCAAUUGCGAGCUGUGACU
UUCAGUAAUCGGUGUUGAUAUUUAUAUUGCGAGCAGUGGCAUACCCAGGACUUUCAGUAA
UCGGUGUUGAUAUUUAUAAGAGAAAGGAUAAAAAUUUAAUCACCACAUUCACAUGUAUGA
UAUUCCUUGGUCCGUUGGUAUAGUCUAGUUUUAAGCUAGAAGAGGUCUUGGGUUCAAUAC
UACUAAACCACAGUUUUUAAGAAAAAAUGCAAAAUAAUGCAGAGGCUGAGGUUCGAACCC
UCAAUGCCAAAGACACAAACACCGCUGAGAGGAUUCUUUGGUCAAGUAGUUUCAUUUUAU
UCAAUAUAUCUCUUUAUCCAUAGUAUUGAUAUUUAUAUAGUAAAAUUUUCCGAUGAAGGG
GUGUUUACCUGAUGUUAAAGAGCGAGAUCCUAUAUCUGUUGAACUUUUUAAUGUUACAUU
UGGUUGACCAAACAUUGGGUUGAGGUUGUCUUGUCUUGCUUCACUGACAGCACUAUGCUA
UGUUUAUUUAUCCAUGAGAAAAUAAAACAAGGAUGGUGGUUCUUGACCCUUAAAAGGCAG
AUGGUACUUAAGUCACUUCAUUCAUGGUUGGAACUGAUCAGCUUUCAGUCAGAAAACCUG
GUGUUCUCAUAUAAACGCAUUAUCAAUCUCCACAUCCAAUUCUGAUCAGCAUUUGAUUCC
ACUCGAUAAACCUGUGAUUAAUUUGUCCCAUGUAGUCUCUCCCCAGUACAUCUCGAGUCU
CUUCUACUCACUUCUUUUUCACGGAAUUCUGGGUGUAUCUAAAGUGGGUUAGAAUUAAGA
UAUUGGAUUUUAAAGAUAAGAAGCAAGUUAAAUGAACCAACCGAUUUUGCAACCUCUCAC
CAAUCCGUAUCGGUUUCUCACUUUCUUCCUAAAAACAAAUUUUGCAUUUUCCAAUGUUUU
GGACUUCCGCUGUUUUCAUUACGUUGGAGUGAUUGAGAACUGCUUUUAUAUCUUAUUUGA
AUUUUUCUAUGCACAUAUUUCUCCUUUAGUUGUGUUUUAUUCCCUAGAAUUUAUGAAGAU
CUUGAUAUUCAUCACUGUUCUAUCUAGCAUGCGUUUUCUCUUGCUGCUAUGUCUGGAAGU
GGCUGUUUAAGAAAAUCAUUCAUGGAUUAAUUGUGAGUACUUUUUGUCUUCAUAACAUUU
UCGAGCUGUUGAAAUGCAGGAGGUUGAGUACUCUGGCGGAGGUUUCCUUUGAAUCAAACA
AAGCUUAGAAAUCUUGAAUUUGGUCGAGAUAGAAAUUACACUUCUUGAAGCAUGAAUUUG
ACAAUAUUUACUUGAUCUAAAUGGAGGAUACAAUACCUUCCAUUUCUUCUCAUGAAUAUU
UAGUAUUAUUGUCUCACAAACUUGCAUGAUCACUUCUCUAUUUUGCUCGUUCUCACUAUA
UCUGAAAUUAGCCAUGAUGUUCUUUUGGAUUAAUGUUUUCGAAGGACCAUUUUUGUAUCA
UGUAGCUAUGGAUACUUAUCUAUGAUAGUUGAAUUUCCAAGCAUUCCCACAUCAGUUCCA
AAUGCAUACGGAAUUGCAAGUGUUUAUUAUUGACUGUACCAUGUUUGUUAAGAAGAAAAA
GGGUAGAUCAAAUUUAUACUGUACUUGUAACAACUCUAUUUAACUUCAAACAUGUUAUGC
AUAUACAAAAUCUUUUAAGGAUCUUAUUUGGAAUCUUCUAAAAGAUUUUUGUUCAACA

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 [-472.99] kcal/mol.

2. The frequency of mfe structure in ensemble 6.24039e-27.

3. The ensemble diversity 461.03.

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