lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-438.20) is given below.

1. Sequence-
UGAGGCUACAUCCUUAGGAUUCAUUUUAGACUAAAUAUUAGAGUGCAAGUAAAAUAAAAU
AUUCAUACAAAUAAUGAAAAAGAGAUGAGUUAAGGAAUGAGCACGGAUUCCAGCCUUAGG
CCAUUUACUCUUUGAUUCUCUAAUGUUCACGCCUUCUCGUCUUUAAGUCCCGAAUCAAAU
UUGGUCUUGGUUGACGAAUUAACCCAACAAGGAUGGUGGAUGAGAGUCCCAACUUGACUC
GGAGGGAGGUUCAUGCAAGAAAAGGAGGGGAAAAGGAUUAGUAUUUGCUCAAAUAUUUAU
AGCCAACUAAUACAGAAAUCACCACUUCAGAUAUGGACAGUUUGAAGAGGCCUAUUUUCC
ACUUCUUUAUCUAUUUUGAAUGCAAGGGUAACUUGAUUAAUUGCAGACCCAACGGGAUCU
GAAAGAACCCACAUAUACAAGCCAUUAAAUCAAGGGUCUAAUCAAUCAUAACAUACGCUU
CCAACUUCUACCAGGAAUUAAGAUGCUUCGAUCCACCCACACGAAUUGAGGCAUGCAUGU
CAUGAACUAAUCAUGCUUUUAACAGAAUGAGACAACAAUGUUUCACAUUUCAAGUUGAAU
GGCAUUUUGAGCAAAUCCUAGGAAGACACCUACUAAGCGCAAUUCAGGAGAUGAUUUAAU
AUCAAAAUUUUACUACAUCAACGAACUUAGUUUGGAUUCAAAUAGACCUAAUACAAUAAA
CCAAACAACACUUAAAAUGAACAGUGAAAGAAGGCAAAUUGUGCAGAUUUCCGUACUUAU
ACUGACUCAAAUCUAUCACCAGGGAGGGACACCACAUAUUCACAGGGACAUGCUGGACUU
AUUCUAUUUCUUUAUCAAAGACGUGAUAUUCUGCCCAAAUAUCUCAUACAUAAUACACAU
AAAUCAUUAUAAUGAAAGUCUAUGUUCAUAUAGAUGCAGGAUUCUGAAACACUUUGGUUG
GGUCAUAAACAAGUCAUCACAUUCUACACUUUACCACAUACUUGAACACACUUAGCAGAU
CUGACAAGCUUAAACUCACUGAAGCAUUUAAGCAUGUAUUAGACUCUCAUGCAUAUACAG
AUAAGCUUUUGUACAGGCAUCAGAGAUAGUGCAAGACUAUGCAUAGCAAAUAAACUUAUU
UCAAUCACCAAAUGGAGAAGAUCAAUAAACUCAUGCAUACUUUCUACUGCCUGAACCAAA
UAAAUCGAACCAACUAAUUUGUCUAGGUGACUUUACCAAAUUCUUCUUCUAUAUUAUGUG
CAGUGGUCAUAUUAUUUCUACAAUUCUAAGGCAGAUGGAUUAGAAAAGUUCUUUCAGUCA
AUAUUAAUGAAGUACUGAUAGCUCUAGGUAAUUUGAACAAAGGAAUAAGCAGUUUAAGAC
CAUCAUUAACCAAGUAUCUACUUGCUAGGCUAUUUAUCAUUCUAAAAAGUAAAUGGAUGU
GUGAAACUGAUACUUCAAACAUGGAUCUAGUCAUCAUAUGUCAAUUAACUUCAGCUAUGG
GAAUAAGAGAAUUGAAAAAAAAGUAACCAAAUUAACAUCAACAAUCAUAUACUGUAUACA
GAUUUAACAUAUGUAAGUAUUUUACCCAGCAAUAUUAUCAAACCACUGAGAUUAUAGGCA
AAACAAUUCAUAAGCCCAGAUUAGCUUUUCAGCACAUUUUAAAGCAUGAAUCAGUCACAC
CAAAGGCAUGGAAUACUGCACAUAAUCAUACCGAAGAAAACUCAGUAUUCAACCAUCUAU
GAAGAACCUUUACUUGAGAGUUGAGAUUGGUAAAUUCUUGAUAUGAGCACACUCAAAGAG
AAAAGAAAAGGGAACCUAUUUACAGAACCUGAACCAAAGUCAAAUCAAAGAACGCGAAGA
GAUCAGUUUUCCUUUUACCAUUUGAUUCAUGCUACUACAUCAGCCAAGAUAUAUAUUCAA
AUCAUAAACACUUAACAGUGUGAAGGUAUGGAGGUCGCAGAUUUACAUACUGAUUCCAUA
AAGAAAGUUGCUCGAAAAUCAUACACUAACGUUAGCAUUUUUGACGGCCAGAAUGAUCAC
CAAGACGCCUCUACCUUAGCUAAUCAAAAAAAAAGGGAGAACUCCUAGGCACAGCUUUAA
ACUCCAACCCUCAUAAUUUCACUCAGUAUUGGAAUACCAAGGAGCUCGCUUGAGGUGAAU
GUACAAGCAAUGCAAUUUUCAAUCAUGAAAGAGUAUGGAGAAUCUACAAAACUUAUCCUG
CAAACACCCUUUCUUCACAGAUAUAUUGGAACAA

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 [-477.64] kcal/mol.

2. The frequency of mfe structure in ensemble 1.61574e-28.

3. The ensemble diversity 615.81.

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