lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-505.00) is given below.

1. Sequence-
UCAAACACCUCCAAAUUGAAGAACACCAACAACAAUUUAUGAAGAUCUUCAAGAACACUU
UGAAACUUCAAAAAUUCAAAUCUCCCGAAACAACUCGGAAUGAGAUGAAACUUGAUAUGU
AGGCUCCUAAUGACUUGUAGAUCACGAUUAUGAACUUUUAAACAACAAACUUCAAAGUUG
AAGAUGGAAUUUCGGAUCAAACGUAGUUACUGUUCAUUUUCUCCAGUUGAAUGUUCAUAU
GAACAUGAAGAACAUGAAGAACACCAAAUUCGAACUCUAUCCGAUUCAACUCGAAAGUGC
ACCAACUUUUAACCACGAAUUCCUCUACUUAUGGUGAAUGAUUUCCACCACUUUUCAGCC
ACGAAUUCAACACGAAAUUACUCCAAUAGAUCCGACCUUGCUUCAAGCUGAAGAACACUU
AGAACACUUAGAACAAUAGUGUUCAAGCUUGAAACCUACUCAAAUCUCAAACCAAAUCUU
CUCAAAUUCGAUUCCCAAACUCUCUGAGAUGUAGAGAAUACGAAUUUCCACCUUUCAAAC
AACAAUAACUACCAAACAACUCCAGAUCUAAGUUCAAAAAUUCGGAUCAAAAGUAUAUUC
AACCACAAAACCCAAUUUCACUUCUAACAUCAAAUCUUCUCCGAAUUUGAUGAAAAUUGA
GGUAGACGAUCCUUGAAACCAAACUUAAUGAUUGAACAACUUCGUUUUUCCAAAUCAAUC
CGAAAAUUUAACAAAUUCGGAAUUUCUUCAAACUCAAACCUUGGAACAAUGGUAGCACCC
CCAAAUCAACUCCAAUUCGACUCAAACUUGAGAUAAUUGACUCAAAUUACUAGGAGAUCA
ACAAAGAACACAAAUUUGAUUCGGAUCAAAUUUUUCGGGAAAAUUCGGAAAAUUCAAAUU
UUGACUUUUUUUUGUGAUUUUUUGAUUUUUAACCAAGGAAUGUAAUCCGUUGAAGCGAAU
UACGAACCUAGGCUCUGAUACCAAAUGAUACGGCCCAAGAUAUGGUCCGUGGAGAUGAGA
GAAGAAGAAGAAGGGAGGGAGAACGGAAAUAGAAGGAUAUGUGGAAUUCAAAUGCGGAAA
CUUACCGUAGUUGAAUUCCGAAUCGACGUCAACGAAAACCAAAUGAUUCACCCACAAAUG
GAGAUUCGUAUUAAUCGACUCAAGUCAAAAUGACUUUCCGAGCAAUUAAGGAUUCACCCA
CCUUAACACUCGAAUUGAGAACGUGGACUCUCGUAAUUUCUAUUGAAAAGUUUGAAAAAC
UACAAUCUAGCUAUUACAUUCAACUACCUAAAUUCUGAAAACUAAAUGUUUAACAAGCAU
AAGCUUCAUCCCAAAAACUCACUACAAUUCAAAUGAGCCUCUAUUUAUAGAGGUACAAGU
UUGUGUAUUACACUUUGAUCCCAACAGUAUCAAAAAGUCACACUUAAGUCCUCAUACUUU
UGAGGCUAGCAAAUUGAGUCCCCAAAGUCUUGUUCAACCUUCCACACAUUGUAGAUCAAC
CCGUGUGGCUCUUCAACAGCCUCCAACACCUCUUUAUGCUUGAAUAAUGCUUGGAAUUGU
UGGAGGUCCUUAGCUUGACUCCUUGUAAAUGGUCUUGAUGGUGUGAGUGUUUUCCGGGCG
UUAUCAAAGGAUGAGUAUUGCAACUUUUGGGAAAGAUGAGGGAUGUAUUUUGUUCGUUAU
UGCAUUUGCCUUGCAUUGGUGCCGUAGUUGAGGGAUGAUUCAGCCACAAAACAUCACGAA
GAAGUUAAGAAACCUAACAUGGGUGCGCGCCUGAUAGUUGCUUACCUUUGGCGCGAAAAG
GUGGAGCUUCGUGAGCUUGAGAGCCUGGGUUACAUUAAUGCUUUGAAAGUAACAAUAGUU
AAUGCCUAAUUGUGAGCGAGGGUCAAGCUAAGCAACGAAUUUCCCUUAUCUGAUGGUAAU
GAUCAAGCUGUGGGUGAGGAUAUGUGAGAAAUUAUUGGAUGUCUUCCACAUUAAUUAGAU
UUGAUGAGGAACCUUGGAAGAUGUGGUUGAAAGGUUCAAUCAACUAAGGCAAACUGGCAU
UGUGGAUGAGUUGUGGAGAAAUAUGAGGUCCAUGAAGGCUCAAAUGCGUACUUGUCCAGC
UUCAUAGGAUUCCUCAAAGAGGCCAGUUA

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 [-541.27] kcal/mol.

2. The frequency of mfe structure in ensemble 2.75399e-26.

3. The ensemble diversity 482.46.

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