lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-524.20) is given below.

1. Sequence-
AGUGCAUCAAUAAGAUUCUUCAUGAGUCUGCUCCUGAAGACUUACAUACAUCAAAAAGAU
UCUUUUCCCUUACAAGGUUAGCCGUGUUGCUGAGGACGACUCUAUUUUUAGAGUGGUAAG
AUCUUAUAAAGGGAUAGCAUGCAGCGUUCGGUGAUCUAGUUUCAUUUGCUUAGUUGGUUA
GACUGAAGUUAGUAUGUUCUUUUUCCCUUGUUAGUCUACUGUCUAUGUUCUUCAAUUUGU
AUUUGAGGUUGGAUGGAAUGUGUCUUUCCGACUUUAUUAUGCUGUUCUCCUGUUUGUAUU
GUGUAGACAUUUGAGUUGAAUGGUCACAAAAGCAAUUUUAUUUUUUGACGAGGUUUUAGC
UUUACCAUGAAACUCUUCCCAAGUUUGAGUGACUUUGCUGCCUGACAAAUUUAGGGAUUU
AAAUAGGGUGGGCUAGGGCAGGUAGCAUUUUGACCCGCUCUACCCUGUCUUGUUUAGCAU
UUUUCAAAUAAAUUCCCCUGCCCUGCUAUGCCUACCCUGACCCGCCCCAUUUACACCAAC
CCAUUAGUGUACCUCUUUUGCACCAGAACGUAAAAUGUUCUUGGAUCCAGCUAGAUCAAC
AAGAUUCAGUUUUUGAUUCUUUAAUGUGCCCACUCUAAACAAACGAACUGCAACUUCUUU
UAGGAGCCAUACCUACAGUUUCAGAUUUGCUAUUUUGGGUUGGAAGUAAUUUCCUAUAAG
AGGGUUAAGUGCUGUAAUUUCUUUGCCAUCAUAAUAUUUUAUCCGUCUAGGCAUCAAUUG
UUAGGUAUAUGCUGUGACAAUUUUCCAUGACAUUUUGUCCAAAACAGUAGUUAGAAAGUU
AUGAUAACUCUAUCAGGAACCAUGAUUCCUUGGUCUCAAUAGCUUUCAUCAGUAAGAUUG
AGAAAUUUGGACUAUGCCCUGCUUUAACACAUUAAAAUUUUUCAAAAAUAAUAUUUUGCC
UAACCCAUCUUCGCUUAAAGCUUUCCCUGCACUGCCCCGGUGUGCCCUGACCAGCCCUGA
CCCAAUUGCCACCCCUAGACAGUUUGAUGUUUCACGAAAGCCUCUGUGGAACAUCCCGAA
CGCAUUUCCACAUUUAAUCUUGAGAUCACAAGGGUGAAGGAACAUCCUAAUGGUCCAUGU
AUGAAUGUUUAUUUUUAUGUUUGAUGUUAUAACCGAGUGUAAUUUUCAUGUCAUGUAUUA
UUGUUCUUUUGCUGUGAAUCCUGGUAAUAUCAGUGUAACUUGGUCUUGUGUGCUUUCAGU
GCUUGUUAUUCCAUGUUCUUAAUUGCUUGUGAUUCGUUUAUCUUGGAUGGUGUAUGCAGG
AAAAACUCGAGUGACAAAUAGUCCUGAAAAUGAUGGUUUAUGUCAAUGCAGUUCUUGUAU
AGAAAUGGGUCAUUUUUUGUGUUAUUGAUGUGCAUAGUGACUUCUAUGAAUCUCAGCAGA
AUUUUCUGAUGCAGGUUCUGACAGUGAUGUAGAACCCCUAUUACAGAGAGGGUUAAACAA
GUAUUGAAAUUUGAAGCAACUCUACCAUUCUGCUAGCAGCAGUGCUCUUGGGUGUCAUUC
GUCCAAUAUGUUGGUUUCCGCAUCAUAAUGUUGUCACCCUAGAGUUCCCGUCUAGUGGUA
AGAUUGUAUCACGUGAUGUGUGUGGGUUACAAGAGCACUCACCAUGGGUUUGAAACUUGC
UGCAAACAAAUUCCUGGUUUUAGGUUGGGGAGAGAAGUGGGGUUGAGUCAAAUUCUUGCA
UCAUGAAUAAAUGAUAAAACUUGCGGAUGGUAAUAGGUGAAUCAAAGUUGAGUUUUGGAU
UGGUCUCUAUCAGCCCUUCAAGAUUUCUCAGUUAUAGAAAGGACACAACAACGGUACCUU
UUUCGUCUAUAAUAAUAGUAAACAAGCUUCACGUGGAACUAUCUUGUCUGAAAAAAAAAU
UGAUAUUAAUGUUAUGCUGGUGUUGCUUGUAAGUUGAGUACAUUGACAAUAAAGGAUCUA
GUUGUAAAAAGAUUGUACAAUGCAUUUCAAAUUGAUAUUUAGCAUAGCUUGAUUUAAAUG
UUUGAAAUAAGAAAAAAGGUAAGUUGUCUUUGUGCAUCUUACUCACUAUUUACGUGGAAA
AAAAA

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 [-562.24] kcal/mol.

2. The frequency of mfe structure in ensemble 1.55898e-27.

3. The ensemble diversity 588.84.

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