lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-340.80) is given below.

1. Sequence-
UGGAAAAGAAAUGUAGUUAGGUUAGUAGAUAUACCACAAAAAGUAGUAAUAUCAAUUAGA
AAGAUACAAGACCAACAAAAAACAAACAACUCUUAAUAAGAUCUGAGCUGGAACAAACUU
GACAGAUAUUUCAAGAUUUUCCUAAUUUGAGAUUGAGGAGAAGAUUAGUAACAUUAGCUG
UUAUAAUUGAAGCCAGAUUAUGCAAAAUGACAGAAAAUAAUGUAAAUGCUUAGACCAUUU
CAGCCAAAAAGAUAGAUUCUUCAUCUUCUCCGCAUAUACCCUAAUAGCCAUACACGUAAA
UGCAAGAACAAGAAGACACAAUAGAACAAAAAAGCAAGCAUCUUGAGAAGAUAUUUCCAC
AAACAAGACCAAACAUGCUAAAAACCAUACACACACCAGAGUAGGAAUCAUCCAUCAUAA
UGGUCUGAUCAGAGACCCAAAAAGGGGACAACUUAGAGAUUUCAAGAUUUCCAAGGUUGA
GAUUAUGGGGAACGGCAGCUCGGUGCACAAAGAACCCCGUGUUAGCAAGGUACGAGGAAG
GCCAGCAUCCCAAGAAGCGAGAUGUAGACAGCUUAUUGACUGGUUCCACCGCUCGAACCC
AGAUACAUGAGACAAUUAAUAAUAGCAGCUGCUGCAGUUGAAGACGGAUUGUGCAAAUGG
GAGAGAAAUAAUGGAAAUGCAGAGACCACAACAGCAAAAACAGAUAGAAUGUUUAUCUUC
ACUUCUUAUAGAUAUCCAUACAAUACAGUAAAAGAAAAAAAGCAAGCAACUUCAGAAGAU
UAUCAUCAAACAAGACCAGCCUUGAUAAAACCAUACACACAUCAAAGUAGGAAGAAAUCC
AUCAGAUCAGUUUGAUCAUAAAACCAAAAAGGGGACAACUUACGAAUCUUACAAGAAACC
CAAUUCUUGCUUCUACCCGUUCGAUCUUUUUUGUUGUUUUGUUCAAGAAAAUAUGAGCAA
AAAGAUGAAAGAAGCAAAGACCAAAAUGUUCAAAAUGGAAGAGAAAUAAAUGGUAAAGCA
GAAAUAACUACAGCAAAAACACGGAUUCUUUAUCUCCACCAUAUAAACAUGUAAGUGCUU
AUAUGAACAAGAACAAAUAAUUCAGUAAACAUAGCAAAGCAACUUCACAAGAUUUUCCCA
CAACCAAAGGCCACCAUCCCUGAAAAAAAACCAUUUAACAGAACCACAACUAAGCAGGAA
GACACACCACGAAGUUGAAAAAGUACCCAUCAAAUCAGUUUGAUCACAGAACCAAAAGUA
GAACUUUAAGAGAUCACAAAGAGCUGACAAGAAACCUAUAAGGAAGACCAGUUCUUGGCU
CGACCAAUUUGAUCUUUUUUGUUGUUUUUCAACAAAAUAUGAGCAAAAAAGAGAAAAAUG
CAGAGACUACAUCGUGCAAAAUGGGAGGGAAAUAAUGGUAAUGCAGAGACUACUACAGCA
AAAAGACAGGUUCUUUAUAUAACCAUCCAUGCCAAUACUUGUAAGAACGAGAAAACACAA
UUCAUUAAAAAAAGCAAGCAACUGAAAGAGAAUUUCCAACAAACAAAAGCCAUCCCUGAA
AAAAAUAACCAUCGAAUCAGUUUAUAGCUUAGUUUUAUGAGAUUACAAACAACUUACAGG
AAACCUCUAGGAAUCCCAGUUGUUUGCUCGACCCAUUUGAUCUUUUUGUUGUUUUUCAAG
ACAAUAUGAGCAAAAAGAGAAAAAAUGCAAAGACCAAAAUCUUCAAAAUGGAUGAGAAAU
AGUGGUAACGCAGAAACCACUACAGCAAAAAGAUAGAUUCUUUAUCUCCACCACCUAUAG
CCAUACAUGUGAACACUUGCAAGAACAAGAAAACACGAUUCAGUGCAAAAGCAAGCAACU
UUACAAGAUUUUCCCACAACCAAGGUUGAAAAAAGCAUGUAACAGAACACACAACAAAGU
UGGAAAAAUUACCCAUCAAAUCAGUUUUUAGCUCAGUUUUAU

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 [-376.97] kcal/mol.

2. The frequency of mfe structure in ensemble 3.24598e-26.

3. The ensemble diversity 537.46.

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