lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-334.30) is given below.

1. Sequence-
AGGAGAUUAGUUUAACAAGAAGAUAAAGUAAAGAGUUGGGUAAAGAAUUCAACAGAAACU
GAAGUUAACCUCAACAGAAACUCCAGCUCAAAACAUGCCAAAAAGAAGAGCAAUGUUUCU
UCCAAUCUUUUUUCUACAAAAAAUGUCCUCACAGAUAUAAAAUACUUGAAUCUCUUAUAU
CCGAAACUAACAAUAAAUGCAGUAUUAUAAUCUCUACAUGUUCUUUCAAUAACCCCAGCA
CUCUUCCAAGUUGCAAAUGGGGGAUUUGGAGGAGCCUCAAAUUCAAGUGUUAUCAAUCUG
CAAAAAUUUUUGAGGAACUAAUGAGGCCAUAUAUACAGAGAUACCCAGUGUUAAACUCUG
CAUCAGUCAUUGGUUUCUGGUAUAAACUCCGUAUAACUGAUACUUUAGUGUAACUUACAC
GAAGAUUGAGGCAUUAUUUUAUAAAGAACAUGUAUUAUUCUCGAUUUUGGCACAUCUAUG
CACGUCAAAACCCUAUAUUAUUAUGCAUAACAUAACAAAAGUUCAGGUAUUAUUAUCUAC
AUAAUAACUAGUCCGCUAGCAAUAGAGUUCGUAAGUGUCCAUCACAUUCAAGAAUCUGUG
AAGUCCAGCCCAGUUUACACUAGCAAAUGUGUAGAAUCACUGUACCAACUAAUCUUAUGU
AACAAUAAGUGGGUGCAUCCCUGUCGUUUCCCUGCAUAUUCUGUCAAAAAGCUACAUCCA
CAGCUAAAUAUCUGUUACCUAAUCAGUGAAACAUCACAAGGAAUCAGAACAGUUUUAUGU
AAAUUGUACAAGGAUCCAAACAAUUUUCCUAUCUACACUGAGGAGUGGAAAAGAAAUGAG
GAAAAAGCUUGGCAGUGCAAUAUCUGCCAAAAAGGUCACCAGACAUUCCAAUACAUACCG
AAUAAGAUAUUAGAAGACUUAAAGAAGUGACCAAUGUUGAAUUCCUAAAUCUCUCAAAUU
UAGAGACUUAACAGUACAGAGAACCCACUACCACUAAAAGAGCAAGAGUUCAUGCAUUUG
AACAGCUAGUGAAAUAAAAUGAUCCGGAGAAUAUCUCACCAAGUGACAAGGAUUUCUACA
AAACUGACACCCAUGGACAUGUAUUUUAGCUAUCACUGCUAGUGGAAUAAUUAUGAUCUG
CAGAAUACACCACCACACAAAAAAGUUUAUACAAAAAAGACAUACACACGCAUUUUAGCA
AUCCAUGCUUCCAAGUACUACUGUAUUGAAAGUGUUUUAUACGAAUUUCACAAGUAUCAA
GAUUUCCUCAUGCCAUGGAUAAUUAAAAAGAAUUACUGCAAUAUUUUCUUUUACGACAGA
UAUUUGGACAACUUAGUUUUACUUCACUCACUGUCUUGCAAAAGAUAUCCCAUGGACAAU
UAAAAAAAACUACUCCGAUAUUUUCUUUUACAACAAAUAUUUGGACAACUUAGUUUUACU
UCACUCUCUGUCUUGCAAAAGCUAUGUCAUAUGAUAGUACCCAUAAAUCAGCUUCUGUCC
UAAAAACUAAACAAGAGAAAGGCACCUAAUUUGAACCAUCACGAGAAAAAUAUAAGGUAA
AACCAAAUGAAGUUGCAGAAUAUAAAAACUACACAAGAAAAAGCCACUAAUUUGAACCAU
CACGAGGAAGACAUAAACAUACAGUAAAACCAAUUAAAGUUGCAAAAUCUCUUUAAAGAU
GGAGGGUUAUAAGAUACCAGCAUAUCUAGGUGACACUAAGUUCAAGUUGACCUGAUCAAC
UGCCUCCCUUCUGCUUGAGUGUUAUCU

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 [-366.25] kcal/mol.

2. The frequency of mfe structure in ensemble 3.06911e-23.

3. The ensemble diversity 498.42.

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