lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-424.50) is given below.

1. Sequence-
UCUGAACAAAACUUAAAAAGAAGAACAAAAAACAGAGAUGGAAAUAAAAUUAUGUCUCUU
UUAUAAAUAAAUUAUGUCUCUCUCUUUUAUAAAGAAAAAAACUUAGAAUGGAACAAAGAA
GAAAGGCAAGAAAAAACAGAGAAAAACAGAAAAUAAAGAACAAGAAAUACAGAAAAGAAA
GGUUGCAGCCUCGCCCGAAGGACUCUACUUCUGAUCGCAGGUCCCCGAAAGAGAAAAAGA
AAAAAACAGGAGUUGAACUGAACAAUUACCGGAAGGACUAGUCGCCGGAAGAACUGAUCA
CCGGAAAUGGUGCCGCAACAGGUUAGCAAAGAUUUGGUAGCUGCUUUUAGUUAGAAACUC
UCAAACUAAUGGAUCCAAAAUUAUUUUUUGGGGUAUGAAAACCCUAAUUUCCGCCAUUUU
UUAUAAAAAAUGAAAAGGCGUCGCCUUUUUGUCGCAUCGUCGUCUUUUCAAAAUCGCCUC
ACCACAGGCUUCAAUGGCGACACAGUCUCGCCUCGCCAUGUCGCCAAAGGCGAAUGGCGA
GCGCCUUUUAUAACAUUGCUUUAAUCAAUUAUCACUCUUGCCUUGUAUGUCACAUCCCAA
GAGAUAAGCCUUUAAAAUUGUUAGUAUAAAAUGAUAAACAGAUAAAGCAUAGGAAAAGAU
UACAAUGACCAAUUUUUCUUCAAAUAUGACCUAUCAAACUCCAAAUGAACUUGGAAUGCA
GAAGGUAGCUUCAUGCCUAUCUUAAAAAAGGGGAAAGAAAAGAGAGAAGGGAGCCUAGUG
UUGUCCUUACUACCCCUCCAGUUCACUCAGACUCCCGGUAAACCACCCUAAAGCAGAAGG
GAGCCUCGUGCUUAUCCUGAAAAGGGGGAAAGAAAAGAGAGAAGAAAACCUAUAUUACCC
UUACUGCCCCUUCAGUUCAGUCAGACUCCUCGCAAACCACCUCCUCUGCACCAACAUUUU
GCAAAAGAGGAUAAAACUCCUACCAUCUUUUGUUUCUCCUCUGGACCUACUAAGAAAUAC
AUGAAAGAUACAAACAGAUAAUCUCCAACAAGCUAAGCAAUCUACAGUCAUCAUGUAUUG
AGGUUUUUCUCUAGUGAAUAUGCAACUGUUCUACAGAGAUGCAUCUCAUGGCUCUAAUUC
GGUUGUCUCGGACAAAACAGUAUUAAGAAGUUCCCAAGAUUUAAACCUCUGACCAAGUUC
AGGUGAAAGUGAUCUUCCUUUCUUCAAGUGGUGCAAAGUCUGAGACCAUUUUCCUUAUUC
GAUGCAAUUGUCAAAUAUCCUCAAAAUUUGUAGUUUUGCCUUUACUUAAGGUAAAUUCCU
GAUCCAUUUAACCAACAAAUGUGUUGUUCUUAAUGAGAAACAGAAGAAAAACACAGAGAA
GGAUUAGGAGUUCAACUUAGCAUGAAUGUACUGCUCCUAUGUUGUUCAAAUGCCAACAGA
UGCCAUUUAGCUGGAAGAGGUGGGAACUUAAGAAGAACGAAACACAAAAUAAAGAGAUGU
GUAUGCAUUAAUAGUUAAAAUAAAAAGAAUGAAAACAAAUCAGAGGGACAACCUGCUAGC
AUGAAUCAAACUAUUUCCUAAACUUCUGCAAACCAACAAUCCAAAUGACAAUUUUAAGCC
CUCAGAUAUAAUCUUGAACUAAUGAAAAAAUCGCAGAUGCCUCACUGUCGCAAAACAAAC
UAGUGCUACUUACAGCAACACUAAACUAACACUUUGAGUAGGCAUUACACUGUGCACUAA
CCUUCCAUUGACUGUCUGCAAACAAUUUUUUAGUAUUAUAUCCACUAAAAUGAUUUAAAA
ACCUAAUACACAACCUAUAUUCACCGAUAUUUCCAUUUUGGAACAUGUAAAAUGGAAAUG
UCAACAAUGUUCCGGACAUCUCAAGGGGGAGUGAGCAAGCAAAACAACCUUACUCAACCC
CUUGAUCAAUAACAGAUUGACUCAAUUUCUUUU

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 [-461.94] kcal/mol.

2. The frequency of mfe structure in ensemble 4.16897e-27.

3. The ensemble diversity 505.90.

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