lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-504.50) is given below.

1. Sequence-
AUAUAACAAUAUUAAAAGUUAUAAAUAUGUUUAUUGUACGAAGUGAGAUGGUUCAAAGUG
AUUUUCAUGUCGAAAGUAAUAGGAAAUAUAGACAUGCCAAAGACAUCAGGAAAAAACAUA
AGCUCUUUUGGCAGUACCAGUUGCUCAGAGAACUAGAAAGAGGCGCACAAUGAACCAGAA
GGCCGGCCCAAAUUGAUCGUAAAUAAUGUCUUCGGACAGCAUAAGCUUUCUGAGAUCCAC
UUCCUGCUACAUCAUUGAGCAUGGAAGCAACGUCCUCAGUGGUCACAUCUCUAGAUCAAG
AGGAAUCCACUGUGAAUCUGAGCAAGAAAAAACCACUAUUAUUUUGUCAAUAUCAUUUAA
ACCACCUUUCUGUCGACAAAACAUUAAAGACGGAAGUUGGGGAUUGCAGCGGGUGAAAGU
AAAGAGAACCUAAUCCACUUGUAUUUGGGCCUGAAAUAACACAUUGUCAUACGAAAUUAG
UCAUUUAGACAUUCUGAUGUUAGUAUAGAAUAACAGAAAGGUGACUGCAUGAUGUUCAAG
GAUAAAAACAUUAAAAACAUCCUGCUGCAUUACAAAGUUUUCUAGGGUAACUAAAUAAGC
AAAAGAGUUGUUGAUUAUGAUACAAGGACACAAAAAAGUCAUGUACCUUGUGGUACUGAU
UUUGGACAUACAAAACUUGUAGCUUAGACAACAGGCUGCAGUGCAGAUAAGCAAUUUCGU
AAGUUCAGAAAUUAUUUCAUUAGGUACAAUUGUCUUCUAAUUUUGCAGUCCAUCAGCCAU
AUUCCAUUGAACCAACUUCCUCUUCUGUGAAACAGGGAAUAGAUCCCAAAAACUGCAAAA
UUACUUGAAUGCGUUCACAUUACUAGGAGAAAAACAUCAUCUGUGGAAAGUCAAGGAGCA
UAAAUGCUGAGGAGAGACAACUUCAGAAAAGAAUCAUAACCCUUGCCUUAACAUCCUUCA
CAUAUCCAAUAGGUGCUACAGUAAAAAUUAAGCAUAGAAAAGAAUCGAGUCUUAUUAGAA
CAACCUAACGAACUUCAUCUGAAUUCCCUUUUUUCGAUUUUGGCCAAAGGAAGGUUCCUC
CUUUAGUGUCCUCACUGCAAGGAAAUACUUCAUUGUUAAAGAAAGGGGGAAAAGAUUGCU
UAGAAUUUAUAUGACAUGAAAGUUACUGAACGAGGAACGAACUUGAGAAAAAGCGAACUG
AACAUCUCGCACAGUAACUUAAGAUACUUCCCUACAAGCUUGACUUGGAAUAGCUGCAAG
CAAGAGUUUGUAGUUUCUUCAAUGCAGAGAAAUAUGUGAUACCUUUUAGUCAUGUGUACU
CCUUAACUCUUUUUUGAUAUAGUAUUACCUUUGACCAGUUAUUAUAGGUUAGAUCACACA
UUUUGACAAAAGUUAUUUUUGUAACAAAGAUUUAGUCCCACACUUGAUGCACCAAAAAUC
AAAUAAAUGACACAUGUAUCAUCAUGGAUAGUCCCAUCCACAAUCUCUUCAUUUAACAUA
AUACCCACAUAAGAUAUGUAAUACACUUUUGUUUUUUGCUCUAUAUGUAUAGUUUUUUGU
AUCACAUCCAUUGUGCUAGAGAAAUAAAAUUAACUUACCAUUGUUCAGAGAUAUAGAACA
CAACUCCAUCACCGUCCAAAUGUUAAAUCUCACCAUAUCCUGUCCACCGCACAAAAGAUG
CCUAAAAGGCUAACUAUUUUUCCUUUUGCCACAAUUCUACAAUCAUGUAGGACACUACUU
CAAACAGCUCAAUAGAUCAUAGAUGCCUCAGGGUUCAUUCAUCUCAUCAUUAUCUUGUUC
UUUUAGUAGUGAAGAAAGAAGUGGCACAAAUAAAAUUGACAGUAGAAACCAAUUCUCCAU
CAAACAAUUUACUCGAGAGACAGAUCAAGAAAUAUCUACAAUUUGCUCCCAGAAUUUUCA
UGGUUAAUGUUCAUAUUUUAUCAUGUCUUUAAAGGUUGCACCUUCCAGGAUCUACUACUA
UUUUCAACCCUGUUUCUCAAGCAGACCAAGUAAUGAAAUCUCACCAACAUUCAUUAUUAC
UUGUUCAUCUACAUAAAAACAACAACAUUACCCACUAAAAUCCCACAAAUUUUUAAUGGU
CUGGGAAUGAUAGAGUUUGUGCAGUCCUUACUACUACCUCUUGGAAGUAGAGAGGCUAUU
GCCAAAGGACCUCGGCUCCAAAGAAAUAUUUUUGGCUAACAUGAAAAGUGAAAUACAAGU
AUCAAACACAGUAAAUUUAUGAUCUAGACAAAUAAAUCUUCAACCAUUCAUCAUGCACCA
UCCCCGUACCUUCCAUUUUGUUCUAUAAAUUUGUGCUUCAAUUUUGUUCACUCUGCUGUA
UUACAUUACGUAACAGAUCCUCUUCAUAGGUGCAAACAUUAAACAUUACGUAACAGAUCC
UCUUCAUAGGUGCAAACA

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 [-548.54] kcal/mol.

2. The frequency of mfe structure in ensemble 9.26064e-32.

3. The ensemble diversity 686.87.

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