lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-614.54) is given below.

1. Sequence-
UUGUACAACUAAACAUAAUAAAUACAAUAGAACGUUACAGAAAAAGGGACCAAUUUUCCU
UCUUUUGAAGAUCUUCAUUUUUAUGUCUUCAACCCAUUGGGUUUGGAUGGAGGCCAACUC
AAUACAAAGAGGAGAACCCAUAUGGGACUCGGAUACGGGAGAGUUCAUGCAUCAAAAGUG
GAAAGGAUUAGAAGAUAAAGAAAUGUAGACUGAAUGAUAUUGUCAAUCAAGCUAAUUAAA
UGAUAAAAAUAGAACAAAUAAAUAAAUCAAUCAAUAAACAAAAGGAUAAUCACAGUUGGG
UAACCUAUAAUAAGAGCUAGUAUGCAUCAGGUUAACUCCAUUACCUCUCAGAAAAAGAUA
AAUUAACCAAAACCUUAGAAAAUCAUACUACCAUUUUCAUUUUGCAACUACAAUUAGUUA
UCUACUACAAGCUCCAUCCAGCCUAAACAGAGUCAGAUAAAAUAGACUAGACUUAAAUAU
GAUGUUUUUCACCAGUCCAUCGCCAAACCAUUAGAUCUUUUAAGCAUUGCAUUAUUACCC
UUUACAAUCAUACGGAGAAUCGACACGUCGAAGUACAUUACAACCUCUCCAUCAUGGCAG
AGGUGAACAAAGGUCAAGCACACAAGUCAUGCAAGAGUGUACAAGGUCUGUUUUCCUAUA
UUCAUUAUUAUGCACAUAAGGCUCAAAUUUGCCAAUUACAGAUUGAAACAGGAUUAACUA
UUAUGAACAUUAAGAGAAAAAAAAUCCAGCAUGCUUAUUAGAGCCAUAGUGCAAGCAAUU
UCAUCACCCUUUUGAAUCUUGCCAAGCCAUUAUAUUGACGACUUACCACCCACUGCUACA
AACAGUGAUAUGCAAGUGCUUUUCUAUUUAUGUUUAGAAAACAAAGAAGGCUUACCUAUU
CGUUUUUUAUUUAAUGCCUUAUCCAUUACAGUUUAUGGCAAAGAUAAUAGCUCAUUCUGA
AGGCAGGCAAACAUAAGUAAUUAAAAUCCAUAUAAACAUGUAUCAGGCAAUCAUGACUCA
ACAUUCUCAUGCUAUUUUCAAUUAACCUUUUGGCAACCAGGGGACUUAUCAUCUUGAUCA
AUCAUGCUAGUAUCACAGAGCCUACUCAAACUUUUCUCAAUCACAAAUAAUGCAACAUUU
AUCUAGAAAACUUAGAAAUAGAACACAUAGAAUCAUUAGAGUGAAAUUUAUACCGUCCCA
GACAGAUUUUCAAGCAAAGAACACAUUUACACAGGAAAGUAAUGACCAGGUUAAUACAGA
AAACCACCGCUUUGAAAUUAAACAGGUCCAAGAGACCCACUUUCAUCCUUGUUCCAGAUU
AUUCCUAAUUCUAUAUACUCCACUGAUGCAUAAACGCGAACAUGCCAAAUUCACAUGAAU
UAACAAGUAUCCAUUCUAAUAACUUUACAUUCAAUAGUGCGCAAACAUAAUUUGGACUAU
UAUCUUCGAUUUUAAAGCCGAUUCAAGCAAGUACGAAACAAGAUAAAGAAAAAAGUUCCA
GUAGGCUUUUGCCAUCACCUUUAGACAUACUUUAUCACAGAUCAAUCAAACUAAAAGAUA
UAAAGUCUAAUACUGACCAUAUCAUAACAAAACUCCAACUUUAACAUGAAACAGUGAUCA
AUACAGUCCAUCCCAAAACAAAUUACCACAUACUGAUUUUAUCACCAGACAUUCACCUCC
UAGCCAUCAUCUUCUCUUAACAUUAGUAUAUCUAGGAAGAAUAGGCAGAUCAACAUGACA
UACUCUUUUUUCAUGAUCAUGCUCAACUCAUUUUGGUAUCAAAGAGGAAAGGCAAUAGCC
AAGUCCUUUUAAAUCCUACUGUUCGAACCCAUGUGAAUUUAGACAAGAAAAGUUAAGAAU
CAGAUUGUCAAACAGCAAAAUCAAUCAGGAAAAAGUAAGAGAACUAGUCAAAGACAGGUG
CAAACAAGGUUGUAUACAAAGAGGGCCACUGACAGGAUCCUGAGAGGAGAGGAAAUAACU
UAAAAGAUGGUGAAUUAUGAAACUCACUCAGCUUCUAUGCCAGAAAUGCUCACGGGAACG
UCCCUACCUCUUCAUACGUUCGAUAAUGUUAACAACCAACCAAUAGGAACACUGUUAUGC
AUUCUAACAUUUUAGUUCCACAACAAAAAGAGCAGUCUCUUAUCAUUCAUCUCAACCAAA
AGAAGACAAAAUCUUACAACAGUUCAACAGGUUCAUUAAUUUGUUCAAAUUGUCAUGCUU
AUCCUUUCAUAGUUGAGCUUAAUAUGAAAUCAUAUGCUGAUAUAGUCCAUUUUAUCUUAA
AGCCUCAACCUUUAAAGAUAACUAUACAAGCUAACUCAAAGCCCUUUCUCUAAGAGUCUA
UCAUGGUAGAGAGAAUCAAGGGAACUUUAGAUUUAGCCACUAAGCUUUACAUGGCAGUCA
AGCAAACAAAACACACUAUGUAACUCGGAUGUAACUAGGAUCGACCUACAUAUCAAACCA
AAUAUAGACUUUGUAUUUUAAAAAAAACAACGGGCAGAAUCAUUACUUUAUUGAACCAUC
GAAAGCAUGCACAAAAUUACUUGAACAAAAUUACCAUGUAUCUCUAUUUGUUCAAAAUCC
ACAGUGAACUACACAGAAACCAAAUUUUCACCUCAAACAUUUGAAAACAAAAAAAGGGCA
AGAUUCUACCUUCUUUUUUCCAACAAACUGAGACUUGAAGAGUUGAGGUAAUUUCCACAG
UUUUAGACCCUACAUUUAGCUUAGAACCUCUCCGAUCCUCCACUCUUGUUGUUAGACACA
AGGAAGGCACCUUAAGUUUCUUGAGGGUGUUAGAUUCACUAUUCUUUUACCUCUCUUUUG
UUUUGUUUUGUAAUAUGUAAACUCUAAAACCUAAAAAUUACUAAGAAAAGCUAGACGCUU
CUUCUUUCUCUUAAAUUCUAAACUUAUAAAUGAAAUUCUUAGUUAUCUCUAUAUGCUUAA
AAAAAAAAUCUAACCCCUUGAUAACUUUCCCAGACAGCUAUUUAUAGGAGGGGUUAAGGA
UUUCUCAAAUUGGGGGGAAAUAAAAAAGGGGCAAGGAUCCCCUUCUGAAAUUUGAAAAUC
AAAUUGAGGGUUUUAGGGGGUGACUAAUCGAAAUCACCACGCCUGUACUAUUCAGUACUA
AAGGAAAGAAGGGUGAGGAGAAACUUACCGUUGUGAACGCUUGACGAAUUCGUACUAUUG
GCGGAAAAAAGACGGAAAAUUGGAAACGUUUGAGAGAAGCUGUUGUUUGGCACUGUAAAG
GUUGUCGUUUUGGUGUUUGUUACUGCUGGACGCUGAUGAG

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 [-677.56] kcal/mol.

2. The frequency of mfe structure in ensemble 3.90312e-45.

3. The ensemble diversity 885.01.

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