lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-638.40) is given below.

1. Sequence-
AAAAAAAACUAAAUAGGAUACAAGAAAAUGAAUCCAUUUUUGGAACGGCCAGGCUCAACA
UCCCUUUUGCUGGAACUAAUGGGUUUUGGACCCAUACUCAUGCGUGAAGAUCACCAAGAC
CAUGAAAAGAAGACAAGGUAAAAACAUUAGAGAUAUAAAAGAGAGACAAAAAAAAAUAUA
GACAAACAAAAAAAACACUUUAUAGAUUUGAAAAUGUCACUCAAAAGGGAUACAACACAU
ACGUUAACUAUAAAGGUCAAACAUAAUAUUUUUAUAGGCUAAUAUGUGAAUAAAAGGCCC
UACUUUUAAGAUAAAUAAGCGACUAAGUCAAAGUUUAAGCAUGCAGCUAUUCACAUAAAA
AAAUAAUUCACCAUAGGGUUGACCGAAUCAUCAUUUAAAGGGGAAUUCACAAGCUAACCC
AAAGUAGGGAGUAGGAAAAGUGAUGCUAGAUAAUAUUAGAUAGUAAAAGGAAAACAUGAC
AAGGAUUUAGAUAUAAAAGAACUUUUGACAAAGCUACUCAGGAUAGAACUAUAGCAAAGA
UGCAUUAUAGCUAACAUCGUUAUCCAAAUAGCAGGCAGUUCAAUGACAAGACAUCACUCA
AAAGUUUAAUAACACCAUUUAGUCUUUAUAGGGUAAAUAAAAUUGAUAUAAUGCUACACA
AAUACAUCAUACACAAGGAAAAGGGGCAUUCAACAGGUUGAUUAGAAUAGACUGGAUGCA
GAUUUUAGGCAGGACCAUUAUCAUAGUCAGCAGGAUACUAUACUGAAUUCACAUAGUGAU
GAUAUACUAUUUAGAGCAGGUUCUUCUAUAUGGCAAGCAGAUAGCUCAAAGUAAUUUAAA
UAGCCAGAAUGAACAUCAUAGCAGACUCAUAAUCAUAUUUUAAUCACAAGAAUAAAGAAA
GACAAACUCUAAACACAACUUUCUAACUUCAGAGCUAUCCCAAAUGCAAGAGGAAACAAG
CAUGCUUGUCAAAUGGAUUCCAAGAAGGAGAAACAGGCAGAUAACAGUUCAAGGUAUGGA
CUAGACAAGAUAUGAUGAUUUUAAAAAAGACUAGAUAAUUCAUGCAAGGUGACACCAAGU
GUUAACCAACAGCACAUAGAUGAUCAAUUCUUUUAAUACAUUAGCAUGCUGUAGAGUCUC
CCAAGAACCAAUAUAAACCCCCUUUAGGCAGUAAGUUAAGACACAGAGUGAAUAUACACA
UGGGUAAUCGUUAAAAUGAAGUAACAUACCAAAGAUAAACAAUUAGAUCAUCUGCAUGAA
ACUAGAGGCAUGGUAGCACAUAUACAUACCAAUACUUAACAAAGAGACAGAUUGAACAAA
UAAGAGUAGGAUAACUAAGUUCAACAGUCAGGUGCAUCAUAUUAAGACAGAUAAGAGUCA
UGCAUAGCAUUUUGAAAAUCAUGAAAUCUAAAACGUAAACACAAAUCCCUAAGAAUUGCA
UAACUCACUGAACUCCUAUCAUGAUCAUCAAGAUAACUUAUUAGGGAUAUUUUCCUGUGU
UGGGGGAGGGACAUCAUAUAGAUGCUUGGCUAUGUCACAGAUAAAUCAAGACUUAACCUG
UAUACAAUCCUCAUUUAGAUAUAUAGAGUCAUCAAUCUCUAAAGAAAGGGCAGUGGAAAU
GUCAUGAUAAUCAAUGCAUAUAACUCCAACCAACUGUUAACAAAUUUGCUUUAUUUUAAG
UCAUCUGAAAUCACCAUCAUCCAACAGAUUGUUCUUAGUCAAUCAAGAAAGACUUUGAAA
ACAUGUCAGGUGAAAGCUUCAGAUAAACAAAUUGAGUUAUUCAAAGGAAUGAAAUUAUCA
CAGCUUAAGGGCAGAGGCCGAGCUGGUAGGUUAUUCAAGAAGUCAAUGAAGCCAAGAUAG
GCAACAUACAAGCAAAUAGAACUCAUGCUAUCCAUGUUUCAUGCAUAUUGGUUACAAGCU
UUAAUGUUUCAGGGGGAAAAAGAUUUAUCUAUCAUACCAUGUUAAUGCAACCAAGAAAAA
UAGAGAUGCCAAUGCAACAGUUUCAUCAUAGAGAAACAGAUUCGAUAACAACCAUUAAAC
UCAGUUAACUAGACAUACAAGCAGUUGAAUAUGCACAGAUUCAGACAGUAGAAUCCAUAG
GACCACAUAGGUUCUUUUUAAGGCAGAAGACUGACUAAAACAUAAAAUAUCUAAUCAGGA
CUAAGUUGGGGGUAAGUGUUAUAUCAAAGACAAAUCAGUCAAACGGGCAGGCUACAUUAU
AGAGAAACAUGCCAAGACAGCUAAGAUGGACUCAAAUAGUAAAAUAUGUGAGCUUGAGGC
UUUAUCAACCAACUACUAUGUUCUAGAUAUCAAACCUGGAUAAGGCCUGCAUUAUUAGUA
AAUAAAAAUCAACUUUUUAAAACCAAAAGACUCUCAUAGAGAAAUUAGCACAUCAGGGAC
AACUUUUAAAAUUAGAUAGUGGGAUGGGUAGAGGGAAAUUAAUAUAGGGUUUUUAGGUGU
CAAGGUGAUUAUAUGAAAACCACUUGGAAUAAGGGAAUCAAAUAACUUAGGAUCACCUUA
CCUUACCUCCAAACCCCAUAGGCAUCCUUGGAUACUUCACUUGUCACUUUUUAAGAAGUA
AAGAAAUUUUUUGAGUAAAGAGACCACUGAAAAGUGAGGUACGAAUAAAACAUAUUCUUU
UUAUGCCAAGAUAGCAAAACAACACCAUGAGACCCCAAAAAAUAGGCCAGGGCAGUAUGG
GGACUCAUCUUGACCAAAACAUCAAUAAAAUAACCAAAUAUAGAGAGACUGGGUAUAGAC
AAGCAAGUGGACAACAACUAGAAUCAGUCAAGACAUCAAGCAAAACCACUCAAAAUGUCA
CAAGCAUGCAGUAGUAUCUACAACAUCAAGAUAAAAGAAGUUCUGCACGGAAUCAAAACA
ACCUCUAGUAUAAGUAAAUUUAAACACUAAACCAAAAUAAGAAACAUGAACAAGAAAAUC
AAAUACUCCAUCAUUAUAAUAUAUUUUAAAGUAACACACUGUUAUAAUACAAGACAUUUA
AUGAACAGUAAACCCAAACGAUAGUAGGAGUUUACCUUUUGGAGUGCAAGAAUCAAGUUA
GGGGUUGGAACUUAGGCCUGAAAAACACUGCGAAACACAAAAUCUCCCCAGCCUUCAAGA
CCCCCUUAAAUGAGUACAAAGAAAGACCCUUUUAAAUACUCAAAGGGGUUGAGGCUCACU
CAAAUUUUACCACAACUUAUCCUUUCUCGGACCUAAAAUAACCUUUAAAGAUGUAAUAAG
CUACGAUUAUUGCUUACAACCACUCUAAACCAUUGUCACCUUCCUAACUUAUUAUUAGAA
UCUAAAAUAGUUUAGCUCUUUGUAUUAAAUCCUAGACUUUCUUUCAGUGCUCCCUAAAAA
ACACCACCAAUUCCUUAUCUAUUC

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 [-700.80] kcal/mol.

2. The frequency of mfe structure in ensemble 1.06985e-44.

3. The ensemble diversity 883.70.

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