lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-607.31) is given below.

1. Sequence-
UUACAAAGAAAGUAAAGGAGAGAUCAAAGAGAAGCCACGGAUUAGGCCUCGGACCCAUUU
UUCCUUCCUGUGAAGGUCUUCAUUUUGUGUCUUCAACCCAUUUGGGGUUUGGAUGGAAUC
UGAGUCGAUUUUGGGUUCUUAGCCCAUUACAUGAGAGAAGAGAGAGUCCGUGGGACUCGG
AGGGAUUUCACAUGGGGCAAAGAAAAGAAUUAGAAGAAAAUCGAAUAUGUAUGGAAAAUA
AGUAAUUAUCUUCCAAACAAAUUAUUAUGCUAUUCAAACAUUUGAGAGACAAUUAACUUG
AAUCACAACGGCAACCUCAGACCCAAACAGUCGACAUAAAAUCCAUCACACAUAAUCAAG
AUAAACAGCUAAUAAGAAGUGAAUGCAAAUGAGGCUUUCAUACAGCACCUAGUUUUAGAA
UUGAUGCAAAAUAUUCUAAUGACCCAUAGAGGUAGUUAGCAGAUGCACAUGUGAGCUUGC
AAGACACAAUCACCAGGUAAUUAGUAAGGGUCAUGCUUAUAUUGAAAAAUAAUAACAUUU
AAAAUUGGAACCUUAAGCUAUAGUUUUAAAAACUGGUGUUCUUCACAACUCAUCUUAGAA
ACCAGUCCAACAGUCUUAUAACCUACACCAUGCAUGACUCGUAUGAGACUCACCCUUCAA
ACAAACUUGCCAAAUGAAUAUUCAUUUAAAAACACAAUGUUCCAGAAAUAAAGUUUUUUA
CAAGGCCAAAGACCAGAUUGUAAAUAAUUGAAUUGACCAGCCCAUUCUUAGAUCAGUCAU
AACAACAUUGCGGCUUUCAAAAGAUAUAUUAGGAUAGGGGCAAGGUCACAGGGAGCUGCU
UACGGAGAUCUGGACUUCACAUAUAUUGUCACUGCCUAUUUUGAUCAGUUUUUAAGUAUA
AAAGGACUAAACUUAGACAUUGGACUAGAUUGUAUGAAAAAUCACAAUAAAAAGUAAUGA
AACGAUUUCCUUGUUAUAAAUCAGACUCAUUUUUAUAGCCAAGACUAACAAGCUCAAGCA
AUUUGCAACACAUUCAAGCGGUUACAGCCUUUUUAGAAUAAAAGAUGAUGGAAGCCUAAU
GUAGCAGCUCCUACACAAACCAAACCAUUUAUGAUCUAUAUGUAUCAAUCAAAUAUCGGC
AACCCAUUCAGCUCUAAUAUAUACAAAUCUGAAAUACUUGCAAAUUGAAAACUAAAACAU
ACAAGUACCUUAGUGGUCAACCAUUUGGAACAUGCUUUUACUUCCAGGAAAACAGACAGC
AAGCAGGGGAAAACAAUUAAGUUACUGAAGUUGAACUCUUAGAGAACUUUUAGCUCCAUU
GAUUUCAAUAUUUUAAACCCCAAAAUCAUCAAGCGGUCCACAGGAAAUAAUAAACGAAAA
UUGAGAGGAGGGAGAAUUUGAAAAGCAACCUAUUAACAGGAUGGUAAUGGCUAAACCUUA
AGACACAAGCAAUACUAACUAAAGCUACAAGAAACAACUAUAGAGUUUUGCAAACCAAGG
GAUUCAGAAUUCACGAAGUAAAGAGCCAGAUUGCUUAUCAAUUCAUGUUAAAACAAGUAA
CUAUGGAAUGUUAUUUUUGAAACAUGGGUCAGUGCAGUCUAGUAUACAAGACUUUAGACU
CUAGUUUAUCAGAAUGAGCUACAGACAGAUCCUUAAGUCUUCUCAUCCCACUGAUCCAAG
CAUUAAUUAGUUCUCUCUCAUGCUAGUGAUAUUGAUAGUAAACAUACAGUGAAAAGAGUA
ACUCUUUAAUCUAAAUAAUUCAGGAAAAAUUUGGUCCUUUCAAGCAUCAUACAUCAAGCA
GUCAUCAAAUCUUUACACCAAAACAUAACAACUUCAUUUCCUAUUUCACAAGAUUAUAAU
UUUGAACACACAACAACACACAAUGACUUAUUAAUCUUUAUACAACUUUAGGACAACAAA
GAGAUCCUAUAUUAACCACUUAAUGACCACAGAGACAUAUGCCACUUUCAAAUUUAAUUC
AUCAUAAGAUCACAACAUUUCAAAUAAUAAACAAGCAGGCUAACAAAUGAGUUCCUUCAC
ACUCUAUUUUUUCUCAUUUCUGCCACAUUUAAUCUUACUAUUUUUUCAUAUAAACCUCAA
ACAUACUCAUAUGUACUUCUUUAUAAACAGCCAAAAAGAAAAAUAAAAUAAAAAAAUACU
ACAUGUUUGCAGAUAAUACAUUAUCCUCAAACUAUUUCUAUAUUAACAUGCAUAUGACAA
CAUCUGAACCAACUGUUCCACUUAAGUGGAGCUUAAACUUACCACUAGGCCAGCUCAACA
UGUUUCGACAUGAAGACUGGUCCACAAACUAUAAGAUGUCUUGCUCAUCAACAUAAAGAU
CAAGAAGUUUUCAGAAAAGGCAUUACAUUAGAGUCAAAGGCAUAUCAUGAAACAAUAAUC
ACAAAAUAGAAACCUAGGGUAACCAUUGUGGUCUCAUAACUGUAAUAUUUAAGCCGUAAA
UGAAAGUAGCACAACACUUCAUUCACAAAUUCUUGCCGAACACGCAUCACAGCAAUCAUA
AGGCACAACCAACAGAUAAUAUGUGAGAAUCAUGUUAAUACUGACAAAUGAACACUCUAG
AACUGAGACCUCAAGCCAUGGUCUAUAUUUUCUCAUUUAUGUCAGCAAUUCAAUCUUAAG
AGAUAAUUUAUCCAGCAAACGUACAUAACCAUCCUUAAUCAGUGGAUUCCAAGCAGACUU
AGGACAUAAAGAAUCAAAUUGAAGCUGAAAUAGUGAACAAAUAAGCAGCUCAUGUCACCA
AACCUGUUUUAGUAAAGGUACUUAACCAACUAUUAACUACCUAAGAGACGCUUAAGCAUA
CUACAUAGGCUAGGUCAAUUUGGCAUUACAUAAAACAUACUCCCAUAUUAUAUCAUAAAA
CACACUCGCAUAUUAUAUCAUUCUUCAUUGUUCCUUUCUAUAACAUGCCUUUCCUAUAUC
AUAUUUUGCCAGCAAAUACUUAAGCAAAUGGCACCAAAAUUCACAUCAGGUUAAUACAAU
GUUCAGCCAGGCCCAGUCUUCACAAAUGGAGAACUAUGCAUAGUCUACUAUUCCAAGCAG
CCAGGAAAUCGACCCCACAUCCACUAAUCAUUCACACCUGUUUACACAGAUACCAGAUGC
AACCAGUACAUAUUACAAUGCAGACAACCAAUAAUGAAAAUUUUUGCUCAAAUGCCAAGA
CAACACUAUAAAAGACCACAACUUUGAUCAUUUGCCAAGAAGGUCCAGACCUAGGGGAAU
UAAAUAAAUUGCAUACCAAUGAAAAGCAAAACAGCAAGUUCAAUAUUCAAAAAUAUAACU
AACAAAAAACUAGCAUAUCAUAUAGCCAAACGCAAGCUUGAAUAACUGGAUAAGCUCAAA
AGGAAAUAAAGGCAGAGAAAGAAAGGUAAACUUGUAUUUUAUCACCCUCUAUAUAUAAUA
CAUACUUUCAGCCUUAUCAGACGU

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 [-672.67] kcal/mol.

2. The frequency of mfe structure in ensemble 8.80843e-47.

3. The ensemble diversity 947.92.

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