lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-594.40) is given below.

1. Sequence-
AACUACUUAUUUGUGAUAAAUAGUGUUUUUUUUUCUUUCUUAUUAUGUGGUUUUCCUUAG
CUAUUUCCUACAACCAUGGUAGGUUCGACUUGCUUUUGUAGCAUAGCUUGCUUUGAUUUA
GCCCUAACCUUAGUCUAUAAAGGGUUUUGGAGGUGGUUCUAGUAUGAUGUCUCUGAAUUU
ACUGCAUAUGAUAUGUAUGACACUGUUUUCCUGUGAUAAUUUGAGUAAUACUGUUGCUUC
UUGAUCAUCUUGGCUGGUUCUAGUUCUUAGCUUUCUUGCUUGUUGAGGUUAAGUGUUUGA
ACUUGAUGGAUGUUAAUGGUUAGUGUUGCUUCUAUGGUAAUCUUAGGUAAAUAUGUUGUG
UUCUUUUGAUUAUGUCCACUGAUCUAGUUGUGCUCCUAUUUUUUGGUGUUAGUUAGUUCU
UAAUAGUUGAGUAAAUGAUUUCUUUCUUAUUGAUAGUAUAUGCAAGAACCUACUACAUGA
UGUAUGAUUGAAAUUGUUUCUGGGGUAACUUUGAACCUCAAAAAAUGGUGUUUCUUGAUU
CUGUCUGGUCAUGCGAUUAUUUUUAGUAGCUUUUAAAAGUUUGAAACAAGUUCUGAUUCA
UGCCUUUUUGUUAUGUGUUCUUCUGUUGAAAUCUGUGACUACAUGUUAGACUGUUUUCCU
AUGUUUUUCCCCUUUUAACUGAUUUUCAUUCAUACUUUACCCCUAAAGUUUUAUGCAAAC
UCUUUUUAAACUAAGGGAUAAAAGUAUCUAAGGUUUCCUAUUGAUGAGUAGGGUAAUGGA
GGCGGUCUUAAUUCCAUUUAAUCCCUUGUUUUCAAGAUGAUACAUAUAGGGUCUCUACUA
GUCCAUGUAUUCUUUGAUUUCGUUCCCCCUGUAAGAUAAAUAUUACAACCUAUGAGGUCU
GCAAGUUUCACAUUUGAAAUGAUCAUCUUGACACCCUAAAAUCAUAAAGCAAAACCCCAU
UAGUCCACCCCAUACUCUGAUUUUCAAGGUUGUCCCUAUGUGAUCCCUUAUUUGCAAAGU
AACCUUCUUAGAGUUUUGUUUUCAGUUUCAAAAGGGCUUUAAGGGAAGUGAAGGGCUUAG
UACUUAUUCAUUUCAUCCCUUCUUUACCUAAACUGCACAAGGACCUGUAUGAGUACAAGG
CAAGGAGAAGGCUUGUGAGAUGGAACUUGGGAAUUGAAUAUUUGUUUUGCCUAUCCUAAG
AACCUAUACCUUGUAAUGAUGCCUAAAGUGAGGGGUGUGGGUCGAUAUGGGGUUCAACUC
ACCUCUAAUGAGUUCAAGGGUAUAAUUAUCUAAAAGGCUGAGGGAUAGAGGACAUUUAAA
UGUCCUCUCCACUGCUUUUGAAGUGAUUUUCAAACUCAAAAAUAUCUUUAUGAAGUCUUG
GCCAUUUUUUCUAUUUUCUAGUUUUAUUGAAGUCAAUAUUGCUUUUCAGUUUUUAGUUAA
CUGCUUUAAUGGUAUCAUGUCAUGUUAUUUUUGUAUCUAUGUGACUGGUCGGCAACAUUC
UUAGGUGUAUUCUGGUUGAUCCUUUCAUAAUGCUGACUUGAUGAAACUAGAAAUGUUUUU
GUGUAUUUUUAAGCUUUUUGAAUCAUGCAUUCACUGGUUAUAUGUUGCUUCUGUAGUUAG
GAGGUCUGAAAUGAUUUCCAUGCUCUAAUGUGAAAUAGUUUGUAAGUGUAACUAGCCUAU
AUGCCUUCCUCCAUUGAAAAGCUUGCUGCAUGCUCAUUCUUGCUAAACUAAUUGAGUAAA
AUUGGAGUUUUUCCUUCCAUGAUCACUAGUAUGAUCUUCACAAUUUAAUAAGACUAUUUU
CCUGGAUUUCUUAAAUUUGGACUGAAAACUGAUAAUACCAAGUCUGUACACUGUGUGCAU
AACCUGCCCUGUUCCAGUUGUAUUUAUACUGUCUAUUUGCUUUGUUUGAGUAUAUUAUUU
GGUUUUUGUGUUUUCUAUGCAUGUACCCUCUCAUGUUAGCUAGCUAACUGCUUAACAAGA
GCUUAUUUGAUCCUACAUAGUCUUCCUACUGCCUGCUAACUUGUUAAGGUUUAUUGGUAG
UUUAAUACCUGCGCAUCUAUAUGUUAUUGGUUAAGUUCAAAUGUUUUUUCAUGUGAGUUA
AAGUAGACUGCUUAAGAGACAUAUAUCAUGCCUAGAAUGUGUUUUGUGACUCGAGGGCCA
GUCUAACAUGCUCAGUAUACUCCCUUCCCUUGAGACUAUCAUGAUGUCUACAUAUUUUCC
UUUUUUUUUGAAGUUGUGUGCAUGAACCUCUCUAUUCUCUUGUCUAACUGAUUCUAUAUG
CAAGACUUGAUCAAGGGUGUGUUCGGUAUGAGGGAAAAUAUUUUUUGAAAAAUGUUUUCC
UAUUUUCCUAUAUUCGUUUGGUUAAUAAUUUUGAAAAUACUUUUCCUAGGAAAACAACUU
CCUUGAAAAUAAGCAAAAUGACUUUCAAAAUAAAAAUAGGGAAAAACACUUUGGAGUGAA
CACCCAUCCGAACAAGUAGGGUCAAUAGUUCAGCAUUUAAGCUGUAACAUAAGUUCCAAA
CUUUUCUACCACCUUCAAAACUAUCCCACCUUCACCCCUACCCCAAACCACUCCCUCUAC
CUUGACCCCUCAACCCACCCCCAACAAUUUUUUUUUU

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 [-641.95] kcal/mol.

2. The frequency of mfe structure in ensemble 3.13564e-34.

3. The ensemble diversity 716.73.

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