lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-626.90) is given below.

1. Sequence-
CAAUUUUAUUAUAAGUCAGCACCAAAGGACCUUAAAAUUCCCCAAUUCGCUUCAUUAAAU
GACAGCAAAAGGCUGAAGAUUCUGUUAGCCUAGUCCUUUGCUCCGUCUGUUGUCGUUAAU
UAUGCAUAGGAUGAGCUGAGCAAAUCUUUAUCGCCUCUACAACGGUAAGCUCAAUUUUAU
CAUUGAUUUCCAGAUGUAUGUGCGUCUCUCCUGUAUAAAUUGAUAAAUGUUGGUGAUAUC
UAAUUGGUUGGGUUUGAAGCCCCCAAAUUCGAAUUCAAAUCUCUUCUUAUAAGCCGUUUG
GUUUGGGAUUUCUGGGAGGAAUUGAAUGUAAUUUCGAAACCUUUCCACUUUUGUCUGUUU
CCCCCCAAAUUUCCUUUCCUUUGAAUCCCUAUUUUUUGGUUCCUUUAUAUACCUCUUUUG
GGUGCAAUUUUGAGGAAGCUUAGAUGUUAGAGAGAAGAAACAUGUAGUCUAAGAAUUCCC
AAAAUAUCAAUUGUUUCUAAGGUCCGAGAAGGAUCCUCAAGCAGCUACACUAUUAAUACA
AAUUUAGAAUACUUAAAUGAUAUGUAUAAGGGGUGAAAUAAAGUCUCAAAGUAAAAUUCA
GCUCAACUUGCUGAAAAUCCCAGCUCCUGCCCUAAAACAGGUAAAAUACUCAUCCUCUCA
UCCAUUUUCGUCACUGUUUUUUGUAAAACAAUGGGUUGUUAAACUUGUAGUGUCCUAUGG
UAAAGCACAAACAUGGCUUGUUUGAGUGAAACAUGCAAUCGUCUUUCCUAAUUUUCUUAC
UGUAUGGAGGAGAAUAUAUGGUUAAGAGUCUAUUUUGGUUGCUUUAUAGGCUUUAUAUGU
GGCAUGUUUAACUAUAAUAGGGUCAUUUAGGUGUGAUUGUUUUGGUUGUUCCCUUUUGUU
GUCUAGCCAUUAUUGUUAAAAGCAUGUAAAGAUCUACCUUUUUCUUUUUCUGGUGCAAGA
UGUGUGGAUAAUAUAUAGAGGGUCUCCUGCUCAUUGUUUACUAGUUGAUCACUUACCUUG
GAUUCUAGUUAAAAUGAAUAUUAGUCCAAUAAAAACAGUUAGUGUUAAGUCUAUGCUAUG
UGUUUCUUUGUUGUCAUUAUGCAUCUGGUACAAGUUUAUGACUUUGAUUAGAUUUUGCCA
AUGUGUUGACCUAUGAAGCUGCUUUACUUGGUUUAUUUGGCACGAUAUCUUUCAUAAAUG
UCUUUUGUUUAAGAAGUAGGCAAUGUCUCAUCUUCUUUUGAGUGUUAAACUAUUUAAUAA
UCUGUGUAGGACUUGACUGCCUAAAUGCCCCUGUUUUAUGUUAAAGAUUGAAGUUUUAUG
GCCAAAGUUAUGUGAUGUGUUGUCAAUUUGAAAGCUAAAUUAUCUAAGUGCAAAAUCAGC
AUAUGUAAUGUUCUUCUCAAGGUUUAUUUGAUUUUUUCUUUUCUCUAUUUCGUGUCUAUA
UUUGGAAUCUGUGAGUCCAUUUGAAUGGCAUCUACCGUUACUUGCCUUUUUUCAUAUGGU
UUUAGCAGUAAAGAUGGGAUCUUUAAGGUCCUUUUAGCAUAGUAUCUUAUCUGUUGAGCC
UACCUGUAUUCAAGAAACCUCUUGCUUUUCUCUAAAACUGUCAUUUCUUCUACUGAAACC
AGUUCCCUGGGUGUUGACGUUUGGUCUGUCAACUCUUAAAUGUUGUAGGGUGUUAGACAU
GCCUAGGUUUUUUAAGUGAAGUUUGUUGACAUGUGUGUUGGCUAUUUGUUUAUUGAGUUU
CAUGGUUAGCUGUUGGUCCUUUCAUUGCCUUAACAUCAUAAAUGGAUGAUAAAAAAGUAC
UUUUCUUUUUUGCAUAUGUUUAAGUUGAGAAUGAUUAGAUGAUAUUGAGAAACUGAUUUG
UAUUUGAAGUUGUUUGUUUGAAGUCUUAAUAAAUAUGUGUGUUCUAAUGAAGAUAUAUGA
UUUCAAUGUUUGGAAAUCAGUUUGUAGUAACCUAUUAAGGUUAAAUACUCUCAUGCUUGC
AUCACUUUCUAUUAAAGUUCAAGUCUUCUGGUCCAUACUACUCAAGUUUUGAUGUGUAGU
UAACUUAUUUUCCAUCUCAUCUAACCUGUUAAAACAAGGUAACAAAAAGAGUCUGCACAU
GACCGAGUGAAGCAUGUCAUCUUUGUUUAUUUUAUGUGAUAAUAUGAAUUGAAGUGUGGA
AUUUUCCUUUCUUUUCCGUGGAUUUGUCACAUGCCUAGGUUUAGGUUCAAUAAUCCAUUA
UUGGAAUCUGAAGAAUGAAAUACAAAUUUUUACUUCUUUGCUUUCUUGCCGCUGGAAAAU
CUGUUAAUGUGUGUAGAAAUCAUUUAAGUUCUUCAUGUUCAAUUUUCUUGAUUUUAUUGA
UUGAUUGUUUAACUGAUUCAAUUAAGUGUUGCUUCAAAUACUCAUUCUGCUUCUCUUUUC
UUUUGCAUGACUCCCUCUUCCGAGUCCAUUUUGGACUCCUUUUUGCUUUAUCGAGUCAAA
CACCUUGCCAAGCCUUCUUUGGGCUGAAGAAAGAAAACAGGAAUUGGGCCUUAGGCCCUU
UGUGAGACGCAGCAGUAGUAGAGAAGUAGAAGAUGGUCAAACCUAUGUAACCUGAAGUCC
AUUAAGAUAGACAUUAAGUAUCUGUUCUCUUAACUUAUUUUCUGCUCAAAUAAAAUCAGA
UCAGAUUCAAUAAAAUCAGAUCAGAUUUUAUCCAGCAAAAUUAAUUUAAUUCAGUUAAGU
UUGUUAUUAUUAUUAUUAUUGUUAGUAAUUAAUUAAUUAUUAUU

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 [-678.65] kcal/mol.

2. The frequency of mfe structure in ensemble 3.39516e-37.

3. The ensemble diversity 657.82.

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