lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-368.40) is given below.

1. Sequence-
UGGCAAGUGUAUGUUUACAUUUAUGGCUGAGUUUUUAUAUGUCCUAUAUUUCCAAGCUAU
GUUAUUUACAUAUUGAAAAUGGGUGAUGCGGCUUUCAUGUCCAACUUGAUCAUCUUUGUA
GUUCUUUUGCAGUGCCGGACAAAAAGUACCUUUCAGUCCUUUUUUACUCAAGGAUGUCAA
UUUUUGUGUUGCGCUUGUUGCUGGGAAUAUCAUCUGUGUUGAAUGUGGAUUGGGGGUUUU
CUUCCUUGGUGCCAGCCUGUUUCAGCUUGCAUUUGCUACUUUCUACAGAGUUUUUGCAGU
AAUUGGCAAUGGCUGAUUGUUUGCACUGUCUUUGUCGCUGAAUGACAGAAUAAACAACUU
UGUACCCGUUCAAUCUAGCUAAAUCAGAAACAUACAGUACACAUUUGCCAUAUGUUAUAA
GCAUGAUUAAUAUACCAAGUUUAGUCAUAUCACACCCUAGUAAAGAAGUUGGGUCCAACC
UAAUCUUGAACACAUGAGUAAAAAUUAGUCUAUGCCGCUCCAAUAUUAGAGCUUUGCUGG
AAAAGGGAGAAAUUAUUGAACACACAAAUAAGCAAAGAGCAGUUUAAUUGAGGCACGCAA
AUACUCACCCAGUAGGGAGGUUAUACUGCAGCAGCACAUACAACUGCUACACUCAUCACC
AAUUUAAGGGAUUCCUCCAAAUCAGAAAAAUCACCUAAAGUAACUCAUGGUAGCCUUAAC
AUAAUUUACUUAUGUGCUAAGUUUUGAUGGCUCUAAUCAAUCAAAAAUGUAACUACAGAA
ACUAAUGUACAUACACAAUAAUUAUAUUCUUGAUGCAAGUUUUACUUUCAGUUCUUUAUA
ACAGACUAAACGAUUACAAACAGUACUUUAAUACACUCAUUUUUUGCUCAUUCUUAAAAC
AAAAAAUAUUAGGUCUAAGUGUCUGACAAAGGAUUAAAGAGAAAUAAAAUUAUAGAAAAA
UAAAGAAACAAGAAACUAGUAUAGUAACAAAAAAACAGAAAAGUAUUGCCUGAAGCAGUG
UGCUGAUCCAAGUCAGCAAAAUGACGAAAAUACACUUGUUAGGAAGCACACAUCCUAAAU
AAGGAAGUAAAUCAACAAGAAGCUGUAGCUGAGAGUUGAUUAAAAUUUCUGGUCCACAAA
CUCUUGAAUUCACUGUCUUUAUACCCUGUGUGAACUUUUCAUAAUAUAUCGAUAAAGUAG
UUUAGUUUAAUUUAAUACAGAGGAAUUCCUUGGAAAGGACUUGUAAAAUAGAAGCAUCUU
ACAGUAGAAAUUAAUUAGAUUUCUGACUUCUGUCAAUUCCACCAUCACAGACCUAACUCC
AAACUAUCGUCUGGCGCUUUUGGGUUUAAAUAACUUAACCCAACCUGCAGUUCCAAUACU
GAUGAAAUCAAUCGAGAAUCCUCAUUUUAAUACUCCAGAUAAAAAUUCCAAAAACUUGAA
UCAGCCAUCACCUAAAAAGAAAUGAGAGAAGAAAUGAACUGAGCAAGUUAAAGCAAACAA
CUCCAAGUGAACUUUAUAGUCUACAAAGCACUGUAACAAUAUACCCAAAUUUUGUUCCCC
UAAAUCAAACUUAUUGAAGGUGAAAUUAACAAACACAGAGAAAAUCACUUGUGGGUCCAG
AUCCCACAGUAACCCAUUCGAAGCUAAGUUCUCAUAAAAUGGGCAAAGAGAAGAUGAAAA
CGCCAUGGCUGCAAAACGAAUCGGUUACAUAACCCGGGAUUCUCAGACCAGAAUUAGCAA
UAGCCUCUUUGCCUCUUUCGAAAGAUGGAAUUUGC

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 [-402.95] kcal/mol.

2. The frequency of mfe structure in ensemble 4.50384e-25.

3. The ensemble diversity 409.25.

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