lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-477.00) is given below.

1. Sequence-
CCAAAAAAUACCAAAUGAACCCUAACUCUUCUCCAGCCGCCCCAUUUUUCCUUUUCAACA
AGGGUACAUUUUUCAAGUUCUAUAGUUGUACGAUGGAAAUGGUAAUAUUCUCUCCAAAUU
CUAGAAUUUUUUUUUGGCAAAUUAUUAUAAUCCCGACAUCUCACAGGGAAUUUCCCAGAG
GCUUCUCGAAUUUCAAGUCAUCAAUCUUCUCCCAUUAAGGAUUUUCAAAUUCAUUUUGUU
AGUCCCACAUUGACUCUCACCCAAAAAAUCCUUAGAUAUUUGAGGUGGUGAACAUCAUUC
UCAACCCAUCAUCUCAUUUUUGCUGCCCGAGAAAAGGUAUAAUAUUCCCUUAGUUCUGCU
UAUUUCUUGAUAAACAAUUCUAUCUGGAUUGUUGUUUGUUUGCUGAAAUUCAGACUUGUU
GAUAAUGUUUUGUAUGUUGCUUUUUGAGUGUUUAUAGGAUGACUAGAUGUAUUUUUGACU
GUGUAAUUAUAUGAGCAUUACCCUUUUCCUGUAAAUCAUUUAAUUGAAGGUUAAAAGCCG
UAUGUAGUCCUAUACCUGGAUAACUUGUUGUCUUAUUCUAAAUAAAGAAAUAUAGGUAAU
UCGAAAACUAUUGUGAAAGGUAGAAAUAAAUAAAGUCAUGGUCAGAAUUUAAUUUGUUCU
UAUUUGCAUGAUUUCAUAGCAAAGAUCGAGUCUUUAUGCUACAAACUAUUUUGAUCUUUU
UGUUAGUCACUGCUUUAAGGGUAAGAGAGUGUAUUUUGUGAAAAGGGAUAGUUCCUUUAU
GAAUAGUUGAGUGUUUUUUGCUGUUGGAUGUAACUUGAAUGUGCAAAAAAGCAUAUUUGG
AAUAGGAAAUGGAUUAUUUGAGGUUGAUUCAUGUACAUCAGUAUGAUUAGAAUUUCAUUU
GGGUCCAAGCAUGUUGAAAUCUGAAGAGUCCUAUGUUAAAGUUUGAGUAUUUAGGGACUA
GCUAGUGUCGUGUCUUGUAUUCUCUGUUAUGGUCAACCAGUUUAUACCCUCUGUUAAGCC
AUGAGCUUUAUAUGUGUGCAAAAAAUAUAAAUUGUUUUGAGUCACAUUUGGUAGAGUUCC
CUUUUUUCUUUGCACAUCAAGAUUGAUAAGGACGUGAUUUUUUCUUUUUUCACAAAGUUG
CCCCCUAUGAGUCUAAAUAUAAUCUGUUGUGAGGCUAUUUGAUCACAUUUUUUCCAUUUU
AAUAGAUUCAAAGGGUAUAAUAUGAAGAGAUUUUUUUUGAGUUUAUAUGAUCUAAGUUUU
UGGACUCAAUAGGGCUUCCUGUUAGUUACCUUUCCUUCUGGUAUGUGUCUUAACUGAUUU
UUUAUUCGCUUGAGUUCCCAGUUUUGUUGAUUACCUGCUUGGUCACUCUUCUAAAUGCAU
AAUUCACACCUUGGUAAUUCCUAAUUUGAGGUUCAUGUGAUUUUAUGUCAUUCAAUAAAG
AGUAUCUUGACUUGCUAAGGUUUAACUUUGAAGUUUUCUCGAUUCCCAAAGGUCACGAAA
GGGUGUUGAACCUCCUCUUGAGACUACUCUUUAUUAGAUUUCUCGGGGAAAGGAGAUUAG
GGGAAUAUCAUGUGAAAAUAGUUUUUGGAAAUGUUUUGAUAUUGUAAUGAUUGGUUUCAU
UUUACCAAAGGUAGAAGCUCCUCUUUCUUCUCUAAAUAGUCAUGUACGUAUGCAAGUUUU
CAAGACCUCGCAAGCUGUCUUUUCCGCAAACUAGUCGUGGAUGCUCUCCCUUUCUUUUUA
UUUGUAUGAUGAGGUAUUUUGAUUAACUUCCCGACAUGUUUAACUAAUUUGAGAACUUGG
AUAAUGAUCACUGAUUCAUUAUUAAGUUUUGUCAAGAACUCAUGUUAAAGAAAAAAAUGC
AUUAAACUCAACCUAAAUGAAGUUGUUUGACACAUUAAGUAUGGAUUUUGGGGUUCUAUU
UACCUCACAUAGCAACCUGGUCUAGGUGAAAUAAUUCAUUGGAAAAUGACUUAGUUUGUC
AAAUGUUAUCUAGCCAUUUUUGUUGCAUGUUAUUUAGUGUUUGAUCGGCAAUAUUGAUGU
UGAUGUUCAUUCGUAUCUCCUCUAGUCCUUAUCUAUAUUUACCUAUAUCAUGUGACAUUU
UCUUGGAGUCUAAAUGGACUCCCUUCCCCCAUUGCAUUAUCCUCCGGCCAAAGCCCAAAU
UCUUGGAGCCGAG

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 [-518.13] kcal/mol.

2. The frequency of mfe structure in ensemble 1.03431e-29.

3. The ensemble diversity 501.81.

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