lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-635.60) is given below.

1. Sequence-
CAAAUAUCCAAAUAAGUGUCACAAUAAAGGUCAAGCCCGACAAGAAUAUCACACAUCAAU
CAUCAAAACAAAAAAUAAAGCCCGACAAGGGCACAAUAUCAAACAUAAUCCAAUAUUAUA
AAGCAGAAAAAUCAAUGAACCACCCUAACAAAAAUAUUGUAGUGCCCUCACUGCCUAUGU
UCAAAUCCUAAGAAGAGUAUGAAAAGAAAGGGGGUGAAGGCUCCUUGUGUUCUACGUCAG
AUUAACAGACCAAAAAUAAAAUGGAUCACUGUGGGGUGAAGGACUGAGCCUCAUCCUCAU
CAUCACCUCUCUGGUCCUCUAACAGAUAUUAAUACUCCUCAUUGUCCUUAUCAUCUAUCA
CUAGGAUCUUCUUGUUCGUCUGCGGCAAUUUGAACAUUGCCUUGAUGCCUUUUCAUAUCU
UCACCAUGAAUUUGCACAUCUUCUUAUUCUUCUCUUUCUCAACCUUCCAAAUUAAUUUGG
AGUUCGACAUGGGCCUUGGUGACAUUUCCAUAAGCUGUCUCAAGUGAAGAUGUUAUCUUC
UAAAGGGACUCUUCCUGCUUCUUCUGAGCAUUCAAAUAUGUUUUCAUUUCAUCCUUGGUG
AAAUGAGCCAGUGAAGAUCCGGAAGCUAUGACACUAAAUCAGACAUAGCACGCAGCAGCU
GAGCCAUAUCACCAAAUGGUCCUCAGUAAGGGCAUUUUAUGUAGUAGUAAUAUUAAUUUU
CCUCUUCUUAAUCUUCUAAGCACUUCCUUCCGCCUUUACUUUCAGACGAUGAUGCUUUAU
CUUGGGCUGAAUCUAGUGGUCAUCGAGGCGCUCAUCAAUAUAUGCCCAUCUACAUAACUU
AGUAUCAGGGACGGGAAUAUUAUGAUUGGGCUAUUCUGUUGCAAAUACUCCCUCAACUCU
CACACAAUAUACUGACCAAUAUUCACAAAAAUGUUGUCAAGAAGUCAAACAACAAUUCAA
GCUCUAAGAGGGGGAACAUCAGACUUUUUCUCCGAAGGAGAAACUCUGUAACAAAUGAUC
UCAAGCCCAUUCUUGCUCAAUUGUUAAGUCACUACUCACAAUCUCUUUCUUUAUUGUGGC
UCAUCGAACCUCUUUCCAUGGAGGACAUAAUUUAGAUACCAGCCACUCCUCAGAGCAUUC
AUCUUUUGCUUGCAUUGUUGAAGAGGGUGGUUUGAAAGCCCAUAAAAUUUAUAGAUCACU
UCCAGCUUGAAUCACACUAUUUUACUCUUUAUGAUUAACUCAAAUUUGAUAAGUCUGCAU
GCUUAAUAUUUGCAUAGAACUCUCUCACCCAUUUUUCAUUUGCAUCACAGGAGGUGGGAA
UGAAACAAUUCCAGGUCAUGGCUGUAAUCCAGCAUAGAAAGCAGGAAGACUUGUUCCAAU
UUAGAGUCCUCAAUGCCCUGCUCUGGUUUGAUUUUCUUGUCAAGCAAGUUGUCAUAGUAA
CAGUGAUGGCAAUCAAGGGACACGAACCUCACAAUAUCAUAGGCAUUAUCCUUAUUUUCC
UUCUCAAUGUAUUGGCCGAUAUCACAUCAUCACCCAGCUCUUGUGCCGUUUGAAGUUUGA
AAGUACCUGCGGAGGACAUGUCACAGGUGUGGAGUCGCUUUUGCAAAAACUCAGUCGCAU
CUACAUACUGUGCAGAAAUUGCUGAUUAUUGCACCUGCAGACGGAUCAAAGCAGAAGCAG
AAAAAGUUCCGCACCAGCAGCUCAUCGUCCUCCAACAAAGUCAAGCACCAAAAAAUGGAG
UCUGAGCAUGCCCUUUUAUCAAUAAUUUGUACUCAAAAUUCUAGAAUUCACAAAUUAUAC
AUGGUCGAACCCUAGAAUUAUUUCCCACGUUUUUAACAAGUAUUACACCAAGAUCGGUGC
CCAAAUUUGCAAAAUUUUCCUCAGCCAUGCCCAAGUAAAGGGUUCCCAACAGAUGAGCAC
AAGGUCGCCUUCAUUAAUCACUUCCAAGGGAAAGGAAAUCAGAAAACAUACCUUAUGUUU
GAGAGAUGACGAAGGGUUUUGUGCCUUGAACUAUACAACCCUUUCUUCUCUAUUUGCUUU
UAUGAGGAGUAGGUUAGUGCAGUGUGUGAGAGUGAUGGAUCAAGGAUAUUUGAGGGGAGA
CACCAGUUGACAGAGUUUUUGAGAAGCAAUGGUUAAGUGUGCAAAUGGAGGGACACUUUG
AAACUGUGCCCCUUUUACCUCCCUGAGAACUAACUUGAUGGCCGCACCUGUGGAGCUUAG
GUCUCUCUUGCGACAUCCGAGGGAUGGAAUAAGAUCUGUACCUACGAUUUUUGAUGACUU
GGGCUUGUUUCACCCUUGCGGAGCUUAAGCCGCUCAUGCGGCUUUGCUGUGGCAAAUAUA
GGGAUCACAGGUGUGACACCCCUGUACUUGGAAGCACAAAUUUUUGGAUACUCACUGUCA
AUUCUAACUAACAGUUUGAGCUCGCCAACGUAACUCUUUACUCACCAAAAGGUCCAGAAC
ACCUCCUUCCAGCACAUUUUACUUCAAAACAUCUAACAUUUUAUUGAUUAAUAAAAAAUA
GCACACUACACUAUUCUA

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 [-679.50] kcal/mol.

2. The frequency of mfe structure in ensemble 1.16771e-31.

3. The ensemble diversity 486.78.

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