lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-551.80) is given below.

1. Sequence-
AAAUCAUUCACCCCUCACGCGCUUCUCUCUCUCUGUCUUCCUACUUUUUCUCAGACCAAG
AACAGCUUGCAAAACCAUCCUCAAGCCCCAAUGUUUUUUGUCAAUCUCUUCACAAAAACG
ACCCUUUUUAAUGCACCAAACGAUGCUAAAAUCUUCGUCAUUUUGCAAACCCCCAUCAAU
UUCUCAUUGGUAGUGUGUUUACCGAGCUGUCAAUCUCUAGAAGCUUCUCAAGGGUAAGUC
UCAAUUUCUAUCACCCAUUCCAGUUGUGAACAUGUCUCUCCCCUACUAGUUUGUACAGGU
GUUUGUACCCUUUGAUUGGUUACUUGUUAACUUUUCCCUUUGAAUUUCAAAUCGGAUUAG
UCCGAGCUGUUUGAUUUCAGAUUUCUAGUACGAAUUCCAUAUGAUUGAGACACCUGUACG
CUUUUAUCUAUGUUUCCCCUUAUUUCAUUUCAUCGUAAGUCCUAGGUUUUGGUUCCUAUA
UCUACCCCUUUUGGGUGCGAUUUUAGGGCAGAGGAAAAAAGAGUCAUUAGUAUCUUAGAG
AGACACUGAGAUUGAUAUCAGGGUUUUUCUCAAAGUUCUCUAAUACUUUAGGGUGGACAG
AUCAUUAUUCAUAGACUAAAGCUCAUAAUCUUACUAAAAGAAAAUAAAGCUGGUAAAAAC
ACUCUUGACUUGCUUGAGAAUCAUAGUUCCUGGCUAAAAACAGGUGAACUACUCAUCUCU
CUUCUCAAUUUCUUUAUUGUUUUGAGUUAAAAUGGGGUACUUGAGUUGUUGUUUGCAGUC
UAGGUGAAAAUAAUGAGUACAUUCUAGUCAAUGUGUUGGAUUCAGAUGUUUCUAUUUGGC
CUUUCAUACUUGCUAUUUGAAUAAAGUGAGAAAUCCUUUAAUUUUUGUUACCUUUUACUG
UUUUCUUAUAAGCCAUUCUCGUAAGUGUUGGUUUGUGAGUCUGUUAGGGUAUUCUUGAAG
UUACAAAGUUCUAUUGAGUGGUUUAGAGUAGAGGUUUGCAUUUUGUGGCCGUUUGGUGUG
UCUCAAAUCAUUUUCUUCCUGUGACUCUUCACAAAUUCUCAAUAUUGUGAAAGAGCCUCC
ACAGAAUCCCCUUUAAUUGAGUUUGCACCUCAGUUGCAUCCUCUUUUUAGGGCUGUAAAU
GAAGGAAGCUUCAUAAUGGCCUCCCUUUUCCUUCAUAGUUCAAUCUCUUGAACUCUGUGU
UUGUCUUAUUUAGGAGUCAUAGGCUUUUUGGCUAUAUCAUGACUCAUGAUGUGUUAAUCU
UUGAUAUUUACCUGAAAUGGAGCCUUAUGUUGUCUGUUUGGUAGGAGGUAAAGAUCCCUU
UUUGUCUUGCAUGCUACUGAGUGAUUUGAGACAUUGUAGCCUGCCUGUUUUUUAUGUUUU
AAAAAAGUAAGGGAGAGUUAGUUGGAAUGUGUUAGUUUCUGUACAACCUACCUAUUGCCU
AAGGUUUAGGGGCCUGUUCAAGUUUGUAUAAGUUAAUUUUUUGACUUAUUGGGUUGCCUU
UAUGUUGUCUGAGGUCUAACAGCAUGUGAAAGCUCUAAUUGAUUCAUUUCCCUAUUUUGU
GUUGCAACUGUCCUUAAUAACUAAAUUUUUUAGUUGUCUGCCUAUAACCACUAAGAGUUA
GGAGGAAAUAGGCAUCUAAGUCUGCAAGCAUCUUUCUACAUUAUGUUAAACCUGACUGCC
UCAAAUCCCUGCUUUCCUGUUUGAGUUGUAAUCUCAUGUAUAGUGUUUGUUGGUUGUUGU
CACUUAGUAAUCAAGGUUAUUGACUCACAAGCAUAGGAGAAUACAUGGGAUUGUUGGUAU
CUUUCUUGUUACCUGUUUGGGAAUUACUGAUUAUAAUUGUCUAUGGCAUGAUAAGUUUAA
AUACGCUCCAACCUGUAUAUUUAUGUCUAAAUUGUAGCCUGUAUAACCUAGUGUGUUGUU
GCUUGCUGUUAUCUUCCAUUUAAAGUCAUGAACAUGUAGGUUUAAGUGAGUAUUCAGAUG
UUGGUUGCUUUGUUUGCUGUUGAGGUUUGUAAGUCGGUGAUUAGGAACCUGCAAAGGCGA
GCCACCAAUUCCAUAAUAUCAUUCUUAAGUUUCAUCAACCUUUAGGAACUGUUAAGUGUU
GGCUUUGUUGUAGACUUUUGUAGGUCUGUUAAGUCCAGUUGAUAAAGAUCAGUCCAGGAG
UAGUAACAUGCUCAAUUUUAUGACUUGCUUCCUUAAUUGUUUUAGAUUCUUAUUUGUUAA
GUUACUUUCUCGUGAAAGGCCAAAUCUCGCCAAACCAAGUUGCCUUUACUUGUUCUUCUU
UUCACUUUGCUUGUUUUAGUGAUUAAACUAUUGUUGCCUUUACUUGUUCUUCUUUUCACU
UUGCUUGU

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 [-594.14] kcal/mol.

2. The frequency of mfe structure in ensemble 1.46199e-30.

3. The ensemble diversity 623.29.

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