lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-444.50) is given below.

1. Sequence-
UAUGUGGGAUCAAUUGCUUAUCUCUUACUCACCUAUUCAUUCCUUCACUUGAGGUUACCG
GUAUACCGACUGUGUUCUCUUUCUUAUCCUCCUUAAUUCCUAUUAUUUUAUUGAGUUAUG
UUUCACAUAUGUUGUUGCAAGGAUACCGGGUACGUUCCUUUCCAUUACCUGAAAUCCUGU
UAUGUGAUUAGCUGGCAUUAUCGGUUUAUGUGACCAUUGGUUGACUCUUGAUAUGCUAGU
UUUCCUGAUUGUCCUAUUUGCUUCUGUGACCAAUAUUCUUGUAUUCUGUUAUUUCCUGCU
UUUAUUAUUGCUAUGCGCUCAGUGGGCCCUCGAAGCCUACUGAGUACAGGUUGCUUCGAC
GGCUUGUACUCAUACUACACUAACACUUGUGCAGAUCCGAGUAUAGGUCCUCGACUGUGA
UUUUCGUGCGGUGAUCAUUCGUUUUGCCCAGUUCAGAGAUCCAAGCUGACUUGCAAUUGA
GCAUCAAUAUGUCCUUGCUUCUCCACUCUUCCUCUUGGUCGUUGUUUCUGGCUGCCUUGC
AAUGCCUGGAAAAUCAUUCAGAUUUCAGAUUAUUUACAGGAAACAGUAACAAAAAUGAAA
UGAAAAUAAUAAAGAAAGAAAGGGUGUGUGCGAGAGAGAUUAUUUCCCCCUUCUUACCGU
CCCAAGGCAUGAGCUGAUCAGCGUUCUUAUUGGCGCGCUGAUCAAGCCUAACCAAAAGCA
AAUUUGACUGGCAUUGUUUCUCUCCGUUUUUAAUUUCAAUUUUGUUGUCUCUAGGUGCCC
UGCUGUAUCAAACAACUCAAGUUCUAUAGCUCUAUUUCGAACAUUUGGACAUGGAAUAAG
AAAUACCACCGUUCUGGAAAGUGGUGCAUCAGAUGCUCAGUUAGUAUUAUAUUCUUCUUU
AAACAACUAAUAUUUUAGGAUGAUUGGAGGGAUCUAGGUCAGUCAUAGCCUACUUUAAUA
CAAUAUUCCUAGGAGCCUUUGGUACAGGAGUUACUUGAAGAAUAUAUGCACCUAAGAAAU
AGAAACAUAUUGCACCCAAUGGUACGGAACCUAGUGGUCAAUGAAGUGGGUUAAAAAACU
AAGGCCAGUUCAAAUUCAAUUCUUUCCAUCUGUUGUUACCUUGGUGAUCAAUGAAGUGGA
UACAUAAUGCUGGUGGGAGGUGACAAGUAUCCAGUGCGAUCUUUCUGCAUCCUCGAUAAG
CAUCCCCUCAUCUGAUUCGUGUACAUGUUCCACAUUGCCUUCACUCUCUCCCCCAUCCAA
AUAAAGAAAUUGUAUUUCUUCUUCUCUCUGUCUUGCAUCACACUGUAUGAUCUAAGCUUU
CUUGCAUCACAUUGUAUGAUCUAAGCCGAAUCAGCAUAAGCUUUCUCGCAGCGUGAUUUU
UCUGUACAACCAAGUAUGUCUUUAUCUCCUCAUAGGUCACAUAACCCUACUGGAACCACG
GUGGCCUCCAGAAGUAACGAGUGGUGGCUGGGACUAGGGUGACAGUCCACGAUCUGUCAG
ACUCAAAGAUCAUAAUUCAUAUCCUUCUGCAACCAGCAAUUCGAUGAAUCAGGGGAACUG
UUUUGCUUUGUGUUCAAGAUAAGUUGCUGAGAAAGAGCAAAAUUGGAAUGUCCAUGUCGA
GAAUCUCAAUAGCUCAGUUGGUUGACUAUUUGCAUUUUCACCUUGUUGUUGGUGAGGAUU
UGAUAGAUGAAAUUUCAAUUCAAACACCAUAUAUUUGUAAUAGAAGUGUAUUCUUCCGCU
AUUGACGACUUUGUAAAUUGUAGCUCAUGUGAGAAUAUAAAAAAGCGUCAUUAUUAUAUA
GUUAACA

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 [-479.47] kcal/mol.

2. The frequency of mfe structure in ensemble 2.26867e-25.

3. The ensemble diversity 435.51.

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