lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-596.20) is given below.

1. Sequence-
CUCUAGCUGUCAAAGCAAAAACAAUAGAAAACCGAGCUCUAAUCCCGUACAGCCGCCACU
AAAUUCCCUUCCUUGACCCUGUAUUUUCAAGCCAAAUCAAAGAUAUCAACGCUCUUUGAG
GGCUAUUUCGGAGCUCUCACUUGCUGUACGAACCCAACAGUAACAUAUCCCUCUCGUAUC
CGAUUUUCUCCAAUUUUUCGUAUGAUUUCGUACAAUCCAGCUCGUCCAACCUUAUGUAUU
AAAUAUUUUGAAUUUUUCACUCCUCUCACAUCACUUGAAAUCCCCAAAAUCCUCAAAUUU
GUCAGCCAUUAAAUACCCCUUCUAUUUACUAUAAAGGGGGCAAAGUUUCUGGCUGAGAGA
ACCCCUAGAAGGUUUAUGGAUUUCUUGGCCUAGAGACUUGAGUCUUAUUAUUUUCUUCUU
UAGAUUUUUCCAUUGCCGGCUAAAAUUCGGAGAUAUAUUGAACUCAUCAUUAGUUGUUCU
GAGAAAUCAGGAGCUAGUGCUAGUUCUUAUUCAAUUUCUAGUCCAAGUUGGAAAGUGGAG
AACCGCUUGUCGUCAACUCAUUAAAUCCCAGUUCCUUCCCAAAAAACAGACCCGAGUGCA
AAUGUUCGACGUUGAUUCUUGAUUGUGAUGAUUAUCCUUAUCUAAGGUAGAUGAUGGCUU
CUGACAUCCAGAGCUACAUUUACAUCUCUCUAUCGUUCAUUUCUAUCAUUUGUAAUAUUG
UAGAUAGAUAUUACAUUUUCACCUCAAACUUGUAUUUAUUUUCUUAGAGGCUUAUGCAUU
AGCUUACUAGGUUUUGGGGAUUUAAUGUACAAAAUUUCUGCGUCUUUUUCCUUAUUUAUG
CUAUUAUCUUUCGCUUUUACUUAUUAUUCUAGCUUUCUGUAUUUGUUAGGGGGUCUCCUA
CGGUGGGAUGUAGGUGCCCUCAUGACCUGAGAAAUCAGGUCAUUACACUUUCCCUAAUUG
AACUGUGGCGUUGAGGUUUGAACCAAAUUGAGUUUUGUUAGUAAAACUAGUCUAGUUUUA
CAUCUGCAGUUGGAUCACCUUUUGCUUUAUGUCUAAAAGUAUAAAUUCAGAGUCUUUAAA
AUUACAAUAGAGUUUUCUGGUUCGCAUUGUUGCAUCCUGUCAGUCCUUGUGCAUCUGGUU
ACAUAAGUUACUUUAGUAAAGGAUGAGUGUUUAUAGUCUAUUUCUUUCUCUCUCUGUUCU
UUAUUGGUUUAAUAAUGCAAUGUGGUUGAAGCUUAAUCGUGUGAGCUUCAAAUGGAAGAA
GAGUUGCUUAAGGUUUAAAUCAGCAUGUGGUAAUGACUUAUAAGGUUAAGGAAUGGAUGG
ACUCCUUGUCCUUGUGUCUAAAGUUGGAAGCUAUGAGGUUUUAUUGGAAGCCAUGCCUUG
CCUUUUUCUCAUUUGACGAGUCUUAUGAUAUACAGAGGGUAAAAGAGACUAUUCGCUUGU
UUAGCUUGUGUACUAUUAGAUUUUCUUAACUACUUGUCUUAAAGAGGAUUAUUUUAUGUA
ACUGGGGAUAUUUUCUUGAUUUUCCUGACGCGAUACCCUACAAACACAACACUAUUUUGA
ACAAAAGGAGAUGGUCCUAACUAGUGAUUGUUUUAAGUUAUUUUGACAAUGUUAUUAAGU
CCUUGGUUAUGAGUACCCAUAUGGACUUACGUGUAGGGGGACUUAACUAAGAUAAGUAAG
UGCUAUUCCCAUUAAAAUCAGUGAAAAUACCUAAGAUAUGGCGUGCCUAGAUAGCGAUUG
CUUUGCUCGACACUCGGUUGACUGCAUCGACAUGCUGCUCAUUCAUAUUAUUUUGUGUAU
UUUGUUAUUUAACUGUCACUUUGAGUUAGACACCAAAGUUAGCCUAUGUAUGUUGCUUUU
UUCUUUAGAAAAGAAUAUUCUUGCUAUUUGAACUCAGGAAGCUCAUGGUCUAAGGUUGUU
AAAACAACCUACAAAACAUAUGUUUUGAAACAUGAGCAGUGUUCGAGUUAGGGUCUUUAA
GAUGGCUUUAUUGCGGUUUGCUUGAGCUUUGUUAAUUUAACUAGUUGACCCCUAUGCUUU
AUUUCAAAAAAUUGUAUUUUCUUUGUUAAUUAGCACUACACUUUUCCUUGAGCUUUGUUU
GGUUACUGUCUAUACGCAUUUCUUUGUGCCCAUAUUGGAAUUGCUUUUAUAGUUACUAAU
CCUCUUUAUAUAUUUUAUUUUUAUGAACUCUUCCCAUCCGAGUUCAAAUGGAAUCUUUGA
UUUGCACUAUAUUGAGUAAAUCCCACAAGCAAGUUCAAUAAGAAAAACAAGAAAUGGCCU
AAGAGCCAUACGUGAAAAGCAAUGAAAAGGAAGGCCAUGAAGCGGAAGUCAAAACAGGCU
UAACCCGAAAAUCUGUAAGUCCAAUGUGGACAAGUUAUAGGGUUCUGGGCCUAAGUGCCU
CAGCCCAACUUCUUAUCUCUCUUUAUGUGGUUGUUUUGUAAUAUUAUUAUGUAAAAAUUC
AUUAUUUUUAAACUUAGACGAAUUCUCG

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 [-639.71] kcal/mol.

2. The frequency of mfe structure in ensemble 2.19387e-31.

3. The ensemble diversity 454.99.

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