lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-557.50) is given below.

1. Sequence-
UUUUAAUCCAAAAAAAAAAAACUCAUUUUUUUAUUUUUUGUAAAAAUUCAGAGAUUUACA
ACAUCCUGGGACCCCACUUGAUUGCGCACAAGUAUAAUAGGGAUACAAAUAUGAGUAAAU
ACAUAAAAGAAAGGGAUAAAGGAAAUAAAAAGCCUUAAUUGGACCGACUCCAAUUCUUCC
AAUCUUGGUCCAGAGCCACAAGUUCAUGCGAGGAGUCCCGGGUUUACACAUGCAAAGGAA
GAAAUUAAAUUAGGGAUCGAAAAUAAUAGGUAAUGAAAUAAAAUAAACAGACAAGGAAGG
AAACAUACCAACACUUUAUGUUGGGAUGGGCCCAAAUAUCCACGGUUUUUAUAGACACAA
UGAAUCCCAAAGAAAUAACAUAACUAAUUAAUGAAGCCCAAUUACAAAAAUUGCGGCCAG
UCGAGUUGGAUGAUCCGGCCUAAUUGCAGAGUCAAGAAGCAUGCAACUAUGAUCAAUGGA
AAUAGUAAUAAGCUUUGAAUUUUAACUUUAAAUAACUGGUAAUAUAUCGUACAUACUCAU
AAAGCACUUAGUUGCAUUUAAGUUAGAAAUUAAUCCAAAAACGGUCUAUUUGGAAAGAUG
GAAACAUAAAGGAUCCAUAUGUAACAUGUUGAGUAAAUUAAUCCAAAGCAUGAGAAUGUU
UGGCAUAGAAAGCAACAACUACCAACUGAAAAGUAAGAAGAAUACAUAUAAUAUCACAAG
GUACAUUGAUUAACCUAUCAAAAGCAUGACUAUCUCCUUAUGAGGAUAUCAAGCCUAUAC
ACAUAACAAAUAUCUAAAAAGGUUAUGCCAAAAUUAGUAUAGGGCAAAAGGAAAGGGAAA
UAGGCCCACAAUCCAACCAUAUAACAGAAUAGCAUGUAGAGUUAGAGGUAAAGGGUUAUG
CAUUUCUUGAUACAAGGAAAUGGUCUAAGGUAACAAGAGGUAAGCUUACACAAAGAUGGA
AAAGUAAUAAAGGUAGAAGAGCGCAAGACUAGACAACUAAAAGUAGAACAUUACAGGUAG
UAGGAGGUAAAAUUAUCUUGGAAAAUGUUAUAUACUCAUAUUUUUUUAGAAGAAAGAAUC
AGAACCUAAUAAAAAGAAAUACUGACUAAGAUAUCAAACCUGAACAGAGUUUGCAUACAG
AUACAGUUAAGAAGAGAGCAUGCAAGUUCAUUUUAUGAGUUCUAGGAAAGGAAAAACAAA
UAAAUAUCAUAAUAGUAUUAAGGGAGGAGGUUUUACUGAGAAAGUUUGUACCAAUAUCAA
AGACCCAAAACAACUACACAGGCAUGAUAUACAAAUUUUAAUAGUCUACCCUAGCUCAUG
CAAAAGGCCUCAGACAUUAGCUAAUUACGCACAUGGGUAAACAGGCAUAAAAUUACUAAU
AACCCUUAAUAGUUUCAACAGGUAGCAAGGUAAUCACAUGGAAUCAGGCAGGUUCUUAUU
GGACAGUCAACUAUCCAACAUGAAAGGAAAUACGGAUAGACAACUCAAAACCAAGCAAUA
UACUAAAUCAAGCAACUAGACAGUAUAAAUGCAACUAAAACAAAGCAGGUGGCUCACACA
CAGUGGUCAGGCUUAGUGUCACCAAUUUUAUAGACCAUAUUCAAAAUAGGUAGUUAAUCC
UAUCAUAUCUUGUUCUGAGGGUUAUAUUAGUUAUCAUAGAGAAGGAACUACUAGUUUUUA
UUCAAUUAACUUAGCAAGAUUGAGCAUAAAGCAAGUUUUUAGCAGGAGUAGACAAGCUAU
ACAUAUAAACAAAUUCUCAUUAGAACACAUAUACCAUUCCAGAGCUACUAAUCAUAUACA
AAUACAACAUAUAACCCGUGAAGGCAUAAUUCAACUUAACAAAUACACACAGUAGAUGAU
AACAUCUCCAAUUUCAACAUAAAGAUAUCAUUAGGCUAGAAUCAGUCAUAAUAUAACCUA
UAUUGCUUAUCAUCCAGUCACAAGAUGUAAAGAAGCAAAACUUAAUACUAUUAAGGUAGU
UUACUAAAAAGGAAAAAGCAAUAUUGUAUCCAACAAUACUGGAAAAAGUAAAUAUGAUCA
AAACUUUGUAAAAGAGGAUUUUAGUUUUAAUUCACUUGAAAAUAGGGGAGAGGAUAUUUA
AAUAUACUUUUUCCCUCAACCUUUCAAAUAAUUAUACCCUUGGACUCUAGAUGUGAGUUG
AACCCUCACCUUAGGUAUCUUCACAAGACUUAAGUCCUUAGGAUAGGUAAAAAAGUAAUA
AAUUUCCCAAGUUCCAUAUCAACAGUCCAUUGCUUAACUUGCACUCAUCUAGGUCAUUAU
AGUUAAAGGCAGGUGAGAAGUGAAAAGACUACAUCUUCACUUCCAUUAAAAUCAGUUUGA
AAUUGAAAAUAGACUCUGAAAGAAUAAUUAACAAAUUAGAGAUCACAUAGGGGCAAUUUU
UAAACCAGAGUAUGGGGGUGGCUUGGGAGGUCUUUAUUUUGUGACUUUAGGGUGUCAAGG
UGAUCAGUUAAAAUCACCUUGAAUAGAAAGAUUAAAUUGGCAUCAGGAUAGCCCUCUUAC
CCUACCUUUCACAUCGGCAUCACAAUGCUUCAUUCAAUAUCAAAAGAUCUCGUCCCUUUG
GGGCUUUGCAUUUAAAUUCGAAUAAGAGCAAACGGGAUGAAAACCAAUCAUAAGACAAUC
GUUGGAUUACAAGCAUACAAAUUAUACUACACGGGCACAAAAGAAAAUACCUCAUCUACA
AGGGAAAAAAUCCCAAAACAGGAUAGUACCAGAGUACAACUUCCACAAAAUAUUAGGACA
AGGUUCAUCCGUGUAGGCGAGCAAGGACUAAUGGUGACAUCACUAGAAACUUUGCAAAGU
AUUGAGUAAAUGCCAAAGGAAAAUGGGGCUUAGGGUUCACGAAUUAGGGCAAGGGAAAAU
GGUAAUGGG

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 [-611.40] kcal/mol.

2. The frequency of mfe structure in ensemble 1.04528e-38.

3. The ensemble diversity 768.12.

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