lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-514.90) is given below.

1. Sequence-
CCCUAGUCCAGACUGGCCCGGGUGCCAAGCUUAAAUUGAACUCUGAAAAAUUAAUUUAAG
AAUUGAAUAAGGGUAAUCCCUAUCAUCUACCCAAGCUAUUAAUAGGGGUGGGCGUUCAGU
UCGGUUAUUAAAACUUCAGUUCGGUUUCGUAAAACUAAUAACCGAACCCAAACUGAAAUA
AAUUCGGUUUGGUUCUGUUUUUGCAAUUUCGGUUCGGUUUUCGGUUUGAGCUUAAAAAUU
AAAAUAUUGGCCUUCAAAAGGAGAAGUGCAAUAAUAUGAGCAAGAACUUCUUGGAGUACU
UAGAUAAUAAUAUUUGGAUCGAUCAACACUAUCCCUGGGACGACGAGGACAAAAGACAGU
UAUUUCAAACUCCAUAGACUAGCAAUAUGUUUGUUCCAACAAAUUACUGCAAAGUGCUUC
AUUCACUAGUUCAGCCAUAACUUUUUUAACAGACAGAUAUACCACUGUCCAAAACACAAA
AUCACACACAUUUAAGCCUAAAGGAACAUUGGUUGGCCCAUUAGCACAAGAAAAUCAACC
AGAUCUCAUCAGGACAGCUUUAACAGCAACAAAAAAUAGAGAAAGUUCUACAGAUGAGCC
UCCAGUAAUCCAAACUUGUCCCAAAUCACUGGAACACCUCCUAACAAUUCACGUCAAAAA
GUUCCACUUUAAGAAAACCGAACCAAAAUCACUUCUCCUUGUGAAGGCCAAUAUUUUUAU
UUUUGAGGCUCAAACCAAAAACCAAACCGAAUAAACCGAACCGAAAUUGCAAAAACCGAA
CCAAGCCGAAUUUAUUUCGGUUCAGGUUCGGUUAUUAGUUUUACGAAACAAAAAACCGAA
CCGAAGUUUUAAUAACCAACCGAAAGACCGAACGCCCACCCCUACACAUUAGGAUUAAGU
GUGUGUUAGACUUUAGUACUAUUUUAGACUUUUAGUUCUUUAAGAAUUUGUUUUAGUGUU
CUACUACCGUCUGCUGCUAAACUAUUUGGAAGAAAAAGACCCAACUACCAAUAGAAGCAC
CAAUAUUACCUACUAAUUAUGUCCAACUAACAAUCCUAAUUCUUCUUUGUUUCUUUGACU
UAACAGUUCUUCUUCCACUUUUGGUGUAAAUAAUGGUUUUUAGAAUAGGAGAUUUCUUUA
AAAGAUUUGAUAGGGAACUGUAAGUCUGUAAUUGUAGGCUUCUGUUUGGUUGUGGUUGUU
UUUCUCUCUAAACAGUAAACAUGGCUUCAGCAGUGCUUUAGUGCUUUCAAUACCAAAAUU
ACCAAUUUAAAAAGAAAAAAGAAAAAAUAUGUCCAACUAACAAUCCUAAUUCCUAAUUCU
GUUGUUUUUUAUGUUUGGAAGAAAAAGACCCAACUAGGUAUUACCAAUUAGUUGGUAUCA
AAAUUAAAUUACAGCGCAAAUAUCAUGUUUUCUAGUUGGCAAAGUCAAGUCAAGGGAUGG
UGGCAUGGUACAAACACCAUGUUACUAAACUAGUAAUGUAGCGUUUCAGGUAACCAAAAA
AAUCCGGAUGCAGUUUAAAUCUAACACAACUGCAUGUCGAAAACUCACAAUACAUUUCCA
AACCCAAGAGCAAGAGAGAAAAUAAAUGCAAUCUAGAAGAUAAAGAAAAAUGAGAAAAGA
CGAGUAUUUCACCUAUUUUAGAGCAGGAACUGAGAUAUUCAACAACAGCAAGUCGAGAUC
ACUAGCAGUGGGUAAAUGGAACUAUCAACUAUAAAAGGAUUGAAGUGAAGACUAGGUAGG
GCACACAUAUAUUGAAAUGCAGAUGCUAGGACAUGCCCCACACAGACGGGGGAAGA

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 [-545.33] kcal/mol.

2. The frequency of mfe structure in ensemble 3.59098e-22.

3. The ensemble diversity 317.27.

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