lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-298.70) is given below.

1. Sequence-
AUCCAAUCCCCAUCCAUGCACCAAGUCAUUCUAUAACAAAACAUCAAAUGGAAGCAUAGC
AGUCACUAUAAUACAACAACAUACCCAUUGUAAUCCCACAAGUGGGGUCUAGGAUGUACG
AAUACCUUAUCCCUACCUAGUGCGAGACCCUUCACUCAAGUAAAAAUAUGUAAGCAAAUC
GAAAAAGGAAAACAAACAAGAGAUCAUUUUUUUCCUCAACCACAAACCACUUUCUUAUAU
UUCAACUAUUUCUUCAAAAUCGAUAAACAAACCCACAUACCAAGUUUUUGUCUUUUAGCU
AUUUCUUCCAAAAAAAACCACCACCCUUUUGCAUCUGAUCAAAACCAACAAAACCCAGUA
CAGAAAAUGUCUAUACAUUUCAAGUAAACAACAUAUAUAACUCGAUGUGGUAGCUUUCAU
CUAUUCUAGCCUUGGUAGACAGAGUUACCUGAUACCUAUUGUUGGUGGGAGGUGAUAGGU
AUCCCAUGGAAUUAGUCAAGACGCCGAAAGCUAGCCCAGACACCACGAUAAUUAAAAAAC
AAAACAACAUAUAUAAUUCGGAUCGACCAAUCAUAAUUCCAAUUUGAAAUUUGAAACCAA
GUUCAAUCUUCAAAAUUCUUUCCCCAAACCAACAAAAACAACAUACCCAUUGUAAUCCCA
CAAGUGGGGUCUAGGAUGUACGAAUACCUUAUCCCUACCUAGUGCGAGACCCUUCACUCA
AGUAAAAAUAUGUAAGCAAAUCGAAAAAGGAAAACAAACAAGAGAUCAUUUUUUUCCUCA
ACCACAAACCACUUUCUUAUAUUUCAACUAUUUCUUCAAAAUCGAUAAACAAACCCACAU
ACCAAGUUUUUGUCUUUUAGCUAUUUCUUCCAAAAAAAACCACCACCCUUUUGCAUCUGA
UCAAAACCAACAAAACCCAGUACAGAAAAUGUCUAUACAUUUCAAGUAAACAACAUAUAU
AACUCUGGUGUUGUUUCUUCCCAUCUUGGUGGAUAGAGUUACGUGAUACUAUUGUUAGUG
GGAGGUGAAAAGUAUCCUUGAUUAAUAAUCAAGGUGCGCGAAAGCUAACCCGGACUCCAC
GGUUAUAAAAAACAACAUCUAUAACUCGAUUCAAUCAAUCAUCAAUUCCAAUUUGAAAUU
UGAAACCAAGUUCAAUCUACAAAUUCUAUCCCCAAAUCAACAACAAACACACUGUGAUCC
CACAAUGGUAUCUGCGGAGGAUAUUGUGUACCCUUACCUACCACUACCUUGUAAUAUAGA
CCCUCGACUCAACUCAAGUAAAAACAUUACAAAGUAAUUCGAAAAAGGAAAACAAACAUG
AGAUCUUCCACUUUUUCCACAAUCAGAAAUCAAUCUCUUAAAUUUCCUCUAUUUCUUCAA
AAUCAACAAAUCCCACAUACCAAGUUUCUGUCUUUCUGCUAUUUCUUCCAUAAAAACAUC
CACCCUCUUUGCAUCUAAUCAAAACUAACCAAAACCCAGUUCAGAAACACCUCAAUAUUU
CAAGAAACCAACAAAUAUAAUGUUUCUUGAAACCGUAAAAAUUCUAGUUUUCAAGAUCAA
UACAUAAGUAAUAUAUGUAAAGGCAAAUCCAAUACAAACUACGAAAAGGGUAUUUGAAAU
UGAGGGAAAUAAAAUCAACAAACCAGUAAAUUUAGCAAAAAUCGUAUGACAGAUCCAAUG
GAGAACUAAAAAAUUCUUGGAAAACUUUCAACUUUUCAACGCACACGCUAUAUAGAUAUG
UAAUAAAUUUUGGAAAAUUAGGAGAGAUUGAGAUAAUUAAUUUGGAGUUGGACUCGGAAU
UGGUGUUGUUCACACUUCCAAAUCACAUAAAUUCCAGAAAAAAUCAGUCUGGCAAUUCCU
CCUCCAUUCCUUUCCUUUUUUACUUUUCU

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 [-335.80] kcal/mol.

2. The frequency of mfe structure in ensemble 7.15773e-27.

3. The ensemble diversity 502.41.

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