lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-413.10) is given below.

1. Sequence-
AGAAGAGGCUACAUCUUUGGGAAUUCAUCUUAGACUAAAUUUAUAAAUUUAUUAGUGUUG
AUACAAACAAGGCAACUAACAUACAAAAGAAAAUAAAAAUAAGAGUUUAAGGGGUGAGCC
UGGGAGGUGGCCGCAGGCCAAUUUAUCUUCCAUCUUUGUUCUUUCAAUCUUCAAUCCGCA
UCAGGCUUGGUUGAGGAGUUGACUCGAUGAAGAUGAUAAUUGGACUCGGGAGGAGGUCCA
UACAAGAAAAGAAUAUAAUGAUUAGUUAUCAAUUCACGAGCAUAAGAUUACCCAUUUAGG
AAAUUAGACAUGUAAAGGCAUGAAAACCAGUUCAAAAUUAGUCACAGAAAUGUGCACAGA
AGAUUGGAUAUUUGAGGACAAGUAGGAAUAAAUUCAGAUGGACAUGGAGAACAAUUUUUA
GGGAAAUAACAUGCUUCAUUUUCUCAUAAAAUCAUUUAGACAUGAACAGAUGAUCACAUA
CAAUUUGAAUAAGUAUAGGACAAACAAGCAUAGCAUGUAGUUUUACGUUAGUAAGUUUAU
GUAUGAGCACCUAUAGGUCUAAUAUUGUAAAAUAAAAAAACUCUAUAGAUAGCUAAUGCU
AUUCCAACAAGCUAAUCAGAAAAUUAAGUGAACUACCUAAUAUGACCAAGUAGCUCAGGG
AUACAUACAUUGAACUUACCAUACUUCCCAACCAUCAAUAGGCCUAUUACUAGAAACUAC
UGUGCAAAAAGAGUUCACAGACCAGGUUUAAGAAACAUUUCAGCUCACACACAAGGCAAA
UGUAUAAUGCAAGGACAAGUGAAAGCUGGGUAGGUUGAAGAACAUAGUGAAAUACUCAUU
AUUACUAGUUCUCAGCCCAGAUUUCAAUAAUUUAGAUAGUGGAUCUUAUUACAUCUAUGU
GAGAGUUUCAUUAAUGAUCAUACAGAAAUAACCAAUUUUUACUCAGUUGUCUUAGCAAGA
GUGAGCAUACAGUAGGUUCUUAGCAGAAAAGACAUGUAGACGGGCUAUAUCUAUAGACUA
AGUCACAUUAGAAUAUAGACACCAUUUCAGAUUUUCAAGUUGAGAUAAGACAUCACAUAA
CUAAUAAAUACAUAAACGAAUAAGCCAUAAAAGAUACUAUACAGUAAAUGCUAAUAUUUC
UAGUUCGUUUAAGAAUCAGGAGUAGAUAGCUUAGGGUUGUCCCAUAGGUAAACAAAUAAA
GGCUUAUUUAACAACAAGGGCACCCUAAACAUCGUUCAUAGCAAUGAUAUAGUCAGGUAU
GCAAGACUAGUCUAUAAGGGAAAGAUUUGCAGACUAAGGCACAUCAAAACAUUUCAACUA
CCCAGAAAAUUUAUGAGCUAUAGAAAUAGACAACACAGUCAAUAAAAAGUCAGUUUAUCA
UACUGGGUCAUACUUCUUAGGUCUUUGAUCUUAAUUGUUUCAAGAACACAUGGUUGCAAU
AAUUCAUAAGCAUAACAGGUUUAGGUUAAGACCAAACAUGAGAAUAUUUGACAAGUAAUU
AAGAAUAUGCAUAGACAACUAGUGUUGAAGCUAGUUUUAAGAGAUGCAAGGGGCAUGCAU
AAAGAAAACUUGAUCUAAGAAAGACAACUAAAAUUCAGGUAUUUAUCAUCCACAACUGGG
GUUAGGGGGAUGCUAGUGUAGAAGACAAAUGCAAAUCGGGGAGGAAAACAUGCUAUCUAU
UAAUUGGUCAAUCUAUUUUUUUAAAGAUCUGUUCAAGACUUUCAAUUAUGACUCAGAACU
GGGUAAGUGAUCUAUUUCAAGCUUUAGGCAUAUGACAAUCUAGGAAAUUAUCAAGGAUGU
CAGUAGCCAAAUAAAUAAUGUCAACAAAAGAGCAUGCAAGCAAAAGGUGCAACUCUCAUU
CCAAUGACGUAUUACACAAAAAAAAAAAAAGAUUCUAAUGGGUCGGGUCUCAAAUCAACA
UAACACAUAUGUCUUAAGCAUGGCAAGUAAGGUUUGGAUGAAACCAAUUCACAUUAUAAG
AUAGAAAUUUUACCCUGAGACAUGUUUC

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 [-453.15] kcal/mol.

2. The frequency of mfe structure in ensemble 5.98481e-29.

3. The ensemble diversity 516.49.

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