lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-715.57) is given below.

1. Sequence-
UUUUUUUUAAGUCAAAAUUAUUCUUAUUUCAAUAAAACUCAGAAAUUACAACUCUUGGAU
CCCGCUAGAUUUCAUACAAGUAUAAACAAUACAAAUAAAAUAAAAAGGGGAAAGAAAUGA
ACUUUUAUUUGGACCGGUUCAAUAUUCGACUUGGUUGGGCCACCGCCAACCAGGCCAUGC
AAAAGAAUCCCGGGCCUAAGGUCAUACAUGCAAGAGGGGAGAAGAAUUAGAAAUUGACAA
UAGUAUGUAAUACAAGUAAAUAAAUGAAACGAGCCAAUAGAGAUCAACGAAACACCAGAA
UCUCACAUUGGACCAGGCCCAACCAAGCACAAUUAGGAAAAUAUAGUAAUGAAUAGCCCA
AGUGAAAAAAAUUCAGCAAAUCAUAAGGUAGAACCGAACUAGGAAAGAUUAAACAUAUAG
GGGUCCAGUAGAAAAAACAAGCAUCUUCGGCCAGUAUUUAAUCUUUGCACAGUCCAGCCU
AAUUUCAUAAUUAUAAUACAAAGAGUCAAGUAAAUAGUUAAAUGUCCCCCUCAAUUAAAC
CUUAAUAGCCAUACAGUAUACACACAAGGAUACUGGGAAAAAUCUAAAUUAAAACAAGUA
UAAAUACAUCAGUAUUCAUUUACCCUAGAGAUUAACGUAAUAACUGAUGUAUUUGUGCUA
AGCAUAAAAUAAGAGAAGUCACAUAAGGCAUGUUAAUCAACUUCUUUUAGGAAAAUGGGG
CUGUUUUGUCUUAGAAAGCCACAGCCCCAAAAAUGUAGACAAGCAAUAUACAUACAGAAU
GUAGAGAACAUAUUACUUGGAUCAUUAUUUACCCCUAAUUAUCAUGCUCAUCUGUUUGGG
AUGACACAAAGCCUACACAGAUAGCAAGUAUAUAGGGGAGUCAUGUAAAUACUUAGUCUA
AGGAAAGGAAAAUAGAUAUAUAGUCUUAACAUAACUGGAACCAACUUAUGCAACAUAUUU
AUAAAAAUCAGGCAGGAUUGAUAUCAGAAAAUCAUACGAACUUAGCACAGAGAAGAGGAU
CCGCAAGAAGCAUGUCUAAAGCAAUUAUCAUACGCUCAACUUAGGGGAAAAUAAGAAGCA
GCUAGCAUGUGAAUAUAAAGAUAUGAACUUAGCACACAAGAGAAUGGGAAGCAGGCAGUA
GAUCAUGACAUAAACUCAGUGCAUGAGAGAGAAAGGAAGAGCAAAUGGCAUGCUUACAGA
AAGCUCCAUAUAAAUAGAAGGGAAAGUAGAUAGUGGUUUACAGGAGGAAGCCUCAAUUCA
GUAUGAAGGAAAGGGAAAUAUAUAACAUGUCUACAUCAUGCAACAUAAACCGGUAUAUAA
AGAAGAUGGCAAACAAAAGGUUGGAAGUAGGUUCAUAAGAAAAGGGAGGGAACUUAGUGG
AAAGGGAGAAUGAGAAAUCAGGAAGACAUGUUUAUAAUGAGCUCAGAAUAGAAGGGGAAA
AAGUAGGCAACAGGUAGCAACACAACUUAGUGGACAAGAGAGCAAAGAAGCAGGUAACAA
UUUUACAAUGAACUCAGUAUGAAGGGAAAGAAAUAGGUAGAAAGUUUUUAGGGAAGCCAC
AUACACUUGAUGUAAAUGAAGAAGAGAAACAUGCAGCAGCUAAUUAACAGCAUGCAGGGG
CUGAGGGGAAGGAACCAUGCAUUGCUGCAAAGAUUCAGCUUAAGGAAGAAAAUAGAUAGA
GCAGGCUUUUAACAUAUUCUAAUCACAUAGCCAGUAAGGGAUCACUAGGGACAACCCUAG
AACAAUCACAAGUGAAUCAGAAAUAGGAAAACAACCAAUGAAUUCAACCUAACAAGUAUC
AUAUGCUCAGAUUCUUUAGACAUAAUUAUGACUUGAUAAAACCGACUCCAACCUAGCUAU
CGGGUUUUGAUCCAAACCUUGCAUGCAAAGUGGUUAAGAGAAAAAGAAACCAAGCAAUUG
GAUGAUACAAUUUUGGUAAAAACACAACUGCUAGGCAUUAUGAUUGUGCAAAGGUUCACU
GAAAAAAUUAUGGAGUAUAGAGUCUAAACCUAGGCACAAUAGUUAACUUCACAUGAAGAA
GAUAUUAACACUCAGCCAAUCUAAAAACAACUAAGCAAGUUAAGAUGAAUAGUAACACUC
UGUAAGCUAGCAGGCAGCAGGAAAGUUACACAAAGCCAAUUUAAGCUUUUACGUAACAGU
UAAAUGUCCAGCAAAAAAGGAGCAGGCAAGCAUAAAGGAGUAACAGAUCAUGAGAACAAG
UCUAAUACAUAACAUAAAAGAGAAUUCAAAGAGUAAUCCAGGCAAUCACAAGUAAGACUA
AAAUUGUAAUUGAAUUUCAAUUUAACAGACAUUGCAUGCUGAAAGAGAGAAGGGACCUAA
UCAGUAAUCAUAUUUGAACCAAACUAGCACAAAGGAGCAGUUGAGGAAACAGGUAGAAUU
AGAAGCAAAGAAGUAAGAUAUUUCUAUGCAGGGCUUGAAUUUGAUGCAGUCAAGACAGUA
CAUGUAUAUAUGUGAGGAUGACAGAUCAUCUAAAGUGUGUUCUAACACAUAGAGGCAGGU
GAUCACAUAAAGGUAUCCCAGGGAAGUCAUAAGCAUAGCAAGAAACAGGGGUAAGACUAU
CCUAUCCAUUAUGACAUGCUUAUACAGAAUUCGAACCUAACAAGAAAAAUUUAACUCAGU
CACAGACUUAACAAAAGCUUACCUAUUAAGUCAAUUAAGAAGAGCACAAAUAAGUUCAUU
AUACAACUUUAGGAAGAGAAGACAAGUAAACAUGGUGGCAUUUACUGAACAGGUUAUAGU
AAGACUUAAUGCACAAAAACUGGUAUUUAGGCAUAGUUAUCUAACUCACACAACAAUACA
CUAGGAGAGAUACAAAUAUGUAAGUAUGUGACCACUACUUGCCUAAUUGAGCAGGGAAUA
AGAAGGUCAUGCAUGAUCUAGUUAAAAUUUAUGAGACAGUCAGACAAUCAAUCAAGAAAC
UCAUACACAUGGAUAGUAUUUAAAAGACUAUCAACAUGUUAAAGACAAAUAAUCAAGUAA
UCAUGACCAUGGUUGUAGAUCUUAGUCCCAGCAAUACAUAAUUGACAUAAAAUUUUAACU
UAAUUUAAGGCAAGCUUAUGCAGUUUAAACCAUCAUACCAAGAACAAACAAUUAGGCCAC
AUAAAUACUACUGAAAACAGAGCAGGCUUCAGUCACAAUAUUUAGACUUAGUACUACACA
CUCUUAGCUUCUAUUUGGACUAUUUUAGGGGAUCAACUUACCGUAUCAAGUUGGGAGGUC
AGAUUACUGAUCAUACAUAAGAGACUACCUUAGUUUAGUUAUUUAACUUAGCCAAAGUGA
GCAUUUAACAACUUAUUAGCAACAGAAAACAAGGAGGCAUGUUAUAUUUACUAAUCAGUG
UAUUUAGGUAGGUAUAUCAUUUCAGGUAUCCUGUAAUAGAUGGAACAACAUGUGACCAGC
AAACACAUAAUUAAUAAGCUUAAAACACUGCACAACUACUUAAUUCCCAAUUUUAUUAUC
AGGUUAAUAUCAAGAAAGAAUCAGUCAGAAAAGGACUUAAGACAUGACACUAGCUAGAAU
AAAAUGCACAUGAUUAACUCAUAGCGUCAUUAAGGCAAAUGAUCAAGAGAAAAAGCAGUA
UACAAGCCUAAUAACACUGAAAAACAUAAGACAAAGCCAAGACUUGAUAAAAAGAAGUUU
UUAACCUUUUAAUUCACUUACACCAGUGUAGAGGAUAUUUAAAUAUCCUCUGUCACUUAG
CCCUU

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 [-776.85] kcal/mol.

2. The frequency of mfe structure in ensemble 6.54129e-44.

3. The ensemble diversity 701.37.

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