lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-561.87) is given below.

1. Sequence-
CCGCUCUACCAACUGAGCUAAGGUCGGUUGCUGUUGGUUCUUCCCAAUGCUAUGGUUUUG
AAAACAUUAAAGAAUGUCUAUUUUUGUUCAAAGAAUGAAUUCCUCUCAAAGCACUGUUGA
AUAAUGUCCAUCAGUGUUAUUAAGAUUGCCUAUUGCAUGAGCUUGAGCAUUUUUUCACUU
AUCAAACAAAGGUAAAAGAAAGGGGAGUUCAUGAUAAUGUUUACCUUCACUUGGAAUCUU
GAUAACAUUAUAAGGUGAUUUUUCUUUGUGAGUUCCAAGAACGAAUUUCUUCCUCCAUAU
ACAACUUCAAAAAUAUGAAGUUGAUGAAGAAACAUUUAAAGUUGUUUAUAAGAUGUUUGG
UGACUUAUCUACAUUUUGGCCUGAACUGUACAUUAUUUCUUCAACCAGAUCUGCUCUAAA
GAAUCCCAAUUUUUCUUGAUCUAUGUGCAUAGCAUCCAUCUAGUUAUUUGUUCUCAUGUC
UUUCCCUUUUGCACUGCUACUUGUUCUACUGUCAUUCUUUCUGCGUUUUCAUGCCUAAGU
AUUGGUUUGAAGUUCUUCUGUCUGUUCUCUAUAUAAACUCUUUUACUCCCCUCCACCACC
CUGGUGGCCCCUUUCUCUUUUUCAAACAUUAUUAUCCGUAGUAUAUACUCUUGAAGUUUG
AUAUAUGAUUGGUAUCUCAAGCCAUUUAUGAUGAUUGGGUGCUUAACUUUUUCUUACAUU
GGUAUAGAGAUGAAAGUUUAAGCCUUUUCCUGGAUUAAGAAAUUGCAGGGAAUCUCACAC
UACUGACACAAAAAUAUGUUUUAUAAGCUGCUUUGCGUACGAUAAUUGAAAUAAAUACUU
UUCAUCCACCUCUUGUUAGAAUGGGAAUGUAUUAUGUGCGAAACCCCUCUUCUCUAGAUU
AAAAUAAUUAUGAAAUGAAGAUGAAAAAUCAAAUCAAUCAGACCUGCCGAUUCGAACCAG
CGACCUAAGGAUAUCUGAUAUCCACUACAGUCCCCCGCGAGCUACAGUCUGUUGCUAUUG
AUUCUUCCCAAUGCUAUAGUUUUGAAGACAUAAAAUGCCCAUCUUGUUGUGUUCCAAGAA
UGAGCUAAGGUUGGUUGCAUUGCAUCCUUCUAAUUAUUUGUUCUUGUGAUGUUCCUUUUG
CACCACUAUUUUAUCUCUAGGUAAUCCUUCUGUAGUUUCAUGCAUAGUAUUGGUUUCAAG
UUGUUGUCUCAUGUCUGUUUGUCAAUGUAAACUCUAUCCUUCCCCUCUAUAGCUAGAGAU
UCAAUCUCACAUUACUGACACCAGAAUAUAAUUUAUAGGUUGCUAUUGCUGAAGAAGCGA
UAGUAAAUGCUGUUAAUGCACUCUUGUCAGAGUGGGCCUAUAUUAUAUGGCAAAUCCCUC
UUCUCCAGAUUAAAAUAAUUAUUUAAAAAAAUAGAAAAAGAAGAUGCCAAAAGAAUCAAU
CCGACCUGCCGGAUUCAAACCAGCGACCUAAGGAUAUCUGAAAGGCUUACACCCUACUAC
AGUCCUCCGCUCUACCAACUGAGCUAAGGUCGGUUGCUGUUGAUUCUUUCCAAUGUUGUG
GUUUUGAGAACAUUAUAAAAUUGUCUAUAUUGUUGUGUUUCACAAAUGAAUUUCCACUCA
GAGCUAAGGAUGAAUCUGUUCACCAGUUGUAUGGAGUUAUGCAAUGACCUUUUAAAGUUG
GGAGCUCAUGCUUAAUGCCUCAUGAGCAUGAGUCUUUUUUCAAAUAACUUUGAUUGGAGC
UCAUGCUAAUGCCUUGAAAAUGGUUUUGUUGCUUGAUCUUGCCUGUACCUUGGAAUUUUG
AGUUUAUCUUACUGAGUGACUUCCACGAAUGAAUUUUGUCUUCCAUCUGCAAUGUUAAAA
GAUAUGAAGUUGAGGAAGAAAGUUUUGAAGUUGUUAUAACUUAUAAGAUGUUUGAUGGUU
UAUCUACCUCUUGGACUGAAGUGUAGAUUAUUUCUUCUACUAGUUCUGCUCCAUAGAAUC
CCAAGUUAUCAUGAUCUAUGUGCAUUGUGGCCUUCAUGUUAUUUGCUUCCAUGUCUCUCC
UCCUGACCACCACCCUGAUGCCCCCCUUUCCCUUAUGCAAAUAUUAUAUGUAGUAUAUAG
UCCCGAAAUUUGAUAAAUGGUUGGUGUUUCAAGAUAUUUGUGACAGUUGAGUGCUUGUUU
UCUUUUGUUGGUAUAGAGAAGCAAGUUAUUGUGAGUCUUGAAAUUCUAAGCCUCUGCCUG
GAUUAAGAAAUUCGUUGCAGGGAAUCUCACACUACUGACACAAAAAUAUAUUUUAUAAGA
UGCUAUUACCAAAGAAAAUGGUAGUAAACUCUUUUCAUGUACCAGUUGUCAGAGUUGGAG
UAUAUUCUAUGGUAAGUUCCUCUUCUCCAGAUUAAAAUAAUUAUAUAUGUAAAAAAAGGA
GAUGGCUAAAGAAUCCGACCUGCCGGAUUCGAACCAGCGACCUAAGGAUAUCUGAUA

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 [-607.47] kcal/mol.

2. The frequency of mfe structure in ensemble 7.39097e-33.

3. The ensemble diversity 656.81.

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