lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-676.40) is given below.

1. Sequence-
AUCAAUUAUUAUGAAAAUUUCAGGAGAAUGGUCCAUCGUACACUUGAGAUGCAUCUUGAU
UCUGCGUGAAAUACCAUUCAUAAAAACAUAUAAUAAGAGAAAUAACAGGAAAGAAAAUGG
UUUGGGCUAACUGGCCCGAUCACUUCUGAGAUCCGUGAAUUGGUUUGCAGCCCAUCAAAC
AGGAGGAGACCAUCGGGAACAUGCAAAAAAGGAAGAAAGUAAAUUACAGAUUGCAUAAAG
CAUGAGAAGCAAAUUAUAAACAUUCUCUAGUUUCUAAAAGAAUGGCUCGAAAGCAAUUCU
UAGCAUAAAAGAAAAAACAAAGAUCAUGCCAUUACCGAAAAGUAUAAGAAAUCUAUCAAU
AAUUAUGGGUUGAAUGGAUGACUAAAGGACUCAAAAUAGUAAGUUGACUAGGGCAUUAAU
UAACUAAUUUGGUCCAUCAAAUAUAAUUAGUAAAGAAAACCAAACGAAACAGUAAAUUUG
CGACAAACCAUAGACAAGGUAAUAAUCUUAAAUAACAAAGAGGAAAUAUUCAGAUUUGCA
AUGCAGAAUCUAUAACUACACUAUCAGACUAGCAAGUAUUUUACAACAAGAGAUCUAACC
CUGUAUGAGUCUUACCACUUUUUAUCAAAUCAAGGCCCCCACAGGUUGAGGUAUCCUACA
GAAAAGAGAGUAUUAACACCAUUUCAUUUUUGAAAUAACUUAUGUAAUCAAUCAACAAGG
UGUUCCAGCGUAUUAUUCAAAGAAAAUAGCUUCAGUAGAACAGUAGACUAGGCUUAGUGA
GAAAUCAGAAAAAAGAAAGAAAGAAUGAUCAUUCACUUGAAUAAAAUAGAUGAUAUAAAU
AAGAACCCAUUAAUGUUAAUCCUUCAUACUCAUGUACUAGUGCUUAAAAUAAAGCUAGGC
GGGGUUAUGUUCUAGCAGAAUCAGACAGUAAGCUUAGGAUAGGAAUUGCAGUCAAAAUUA
GGAAAUAAGGCAAUAUGCUUAGGAAUGGAGGUGGAUAACAUAUCAUGCUUAAGUUGCAUC
AAAACUAGACCUAAAUACUACCUAAAGGAAGACUACAAGAUUCACACAAAAUCAAAUGAC
AUGCAUCCAGAUAGUCAUAUAAGAACACGAUCAUUUCUAUUACAUGUAUAACAAAUAAGA
AUAGCUAUCACUGCAGAUUUUAGAAUGAGAAGCAGCCAUGCUCAUAUACUCAAAAUUACA
CUAGUGUAAGCAACAUGUAACUUAGUUCUAAUUCUAUAUUUAAAAAAUUCAAGUUUUGAC
UUGGACGAAAAGGAAGAAACACAUACAACAUCUUUGAUCCUGCUUGGACAUAUGGUCAUA
UUUAUAGACAAUUAUAAAAAAUUAACAUGUAAGAGAGAAAAUGGGAAAACAAUUAUGCUA
GAAAGAGCCAAAGAUCAUCAGGGUGCACAGUUGAGACAGGGACUAUGAUUUAACAUACUA
ACAUGUGUAGCAAGAGAUAACUAUUAACUUAUGAGAAAAUAGACAAGAUAUUUAGAUCAA
AUUCAUAAUAAAUAACUUAGAAAUGAUCUAAGGUGCCAGAGGUGGAUAGUAGCAGGAAAU
AAUAUAGACAAAUCCUGUAUUAUACCCUUAGAAGUAGAACUUGAUGGAGGUCAAGCAUCA
AACCACCCCUCCCAUGUGCACAGUUAAGGGGAGGAGAUUUAGUAGAUUCAAACAUAUAGA
CUUUUUAAGAAAAAAAAGAGAUGAAUGUUAUGCCAUUUCAAUAGAAAUAUUUUAGCACUU
AGCGGAUAAUACUGAGAUUUAGUCAAUUGCACACAAAGAUGGAUGAAUAUACGCCUAAUA
CCUUUAAUGAGUCUACAACUAUCGGGAAGCCACAGAGCAUCAUGCAAAUUUUCCUUGGAC
ACUAGAUUGGUCAAACAUGAGAAGUCCAGGCAAACAUUAACAAAACCAGAUAUGGUAAAU
UAUAUUCUUAAUGUUUAGGUUAAAAGAUAGACAAUAUCUAGUUUCAAGUUAUAAUAAAUC
AACCACCAGUUAUUAAUCCAGUUGAGAUGGAAAAUCACAUUUAAACAAGAUCAGGUAUCA
ACUAAGAUAGUAUUCCAACAUAUAGAAAACAAGGAUAUGGAACACAAGCAAGGAGUUAAC
AUGUUCAGUUCCACACCAACCUUAGUCUAGAAUACUACUUAAAAUAAAGUCAUGCAAUCA
AAUAUAUACAAACAGACAAGUAUGUACUUCACACAUAGUCAUGUAAUACCCUUUUCCAUC
UCAAGAGAAGAAACAUGCUGUCAUUUUAACAUUGUAGAUCAAUUGGGUGUAAGGGGAGAU
UAUCUUUACAUCAGUUGUAGGAAGGCUACCAUAAAGGGAAACAAGCAGAGAUGCAUAUAA
GGAAAAUUCAUGGAGUCUACACACAAAUAACUAUCAUUUUAAAGAUUAGGAAGACAUUUA
CCAAAUAAAGAGAUCAUUAUUAAGUGAGUAAUUAGACUCAGGUGAGUAUUACCUUAGUUU
UCAAAAUGGGAGCAUAAGCUUAAUAGCACCAGACAGUGAGCAUCAUCAUCCUUGUAAGAU
UGAGACCCUUUAACAAUUAUCAGCUUAGAGACUAGAUAUUUAGCACAAUAAGCAAGAAGG
AAAAUUGAGAAGGAAAAAGUUUGGAAAACUUUUAGGAGACAUUACAAGCCCCCACAUCCC
UCAACCCUUAAGAUUCACACCUUUGGCUUCGUAGGUGAUUACUUAGACCCCACACUAAGU
CAUACACCUUACCCUAGGUAAUCUUAUAAUAUAUAAGCCUUUAGAUAAGUAAAGUGUCAC
UAAACCAUAUCAUAGGCUAUCUUAUGAGUGUAGCAAGAACAUUUUAAGACGAAAAGACCU
UCAAAGAGCAGUUAGCGCAUAAGACAUGUAAGAGAUAGUUUUAAAAUAAGAGAGUGGGGU
GGGUUGAGGGAGAUUGAUGUAGGGAUUGUAGGUACCAAGGUUGUUAUGAGAAAACUAGCC
AGAAAUAGGGAAAGAGUGGCCUGGAUUUUCCUCCCCUACCUCCAAUCCCAACGGAAAACU
UUGAUGGUUCACUUGUUAAGUGUAAAUGAAAGGAAAGACAUUAGAAAGUAGGAAAAGAAC
UAUUGACAAGUGAUGCUUGGAUAAAAACAAUUUUGACACACUUGAGUCAUAUAACAUAUU
CAAUGAUGGAAAUAAUUUUGUUUCGAAGACUCUGAACUAUACAUGGGCAGACCAAAGCAA
CAUAAAAGUAAAUAUUGUUAGGAUCAAGCUGGUAGAACAUAAACUGACUGACAGGUUAUG
AAGCUAGAAAAGUAAACUCUCCACAAAGUUUAAACACAAAAAACAACCUCGUAUUCCCUU
UAAGCAAAUUUAACCGUCAAGCCAAAACAAGAAGCACUAAUAGAUAAGUAAGAGAUGCCA
UUACUAUAGCACACUCUAAUGUACCACAUUAUGUCAAAAAACAUCAAAGAAAUAAGAAGA
GGUGAACAGUAAAGAGAAAAGGAUGGUGAGAUACCUUUUAGAGUGCA

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 [-739.43] kcal/mol.

2. The frequency of mfe structure in ensemble 3.85071e-45.

3. The ensemble diversity 829.29.

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