lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-712.30) is given below.

1. Sequence-
CUCCAGACUCGAACCAAAAGUUCAUCUAAACCAAGUCCACAUUCCGAAACUAACAAAACU
GUUAGAAUUCGAUUUCGAAUUCAUUUUCACAAAAUGUAAGUCAAUCAUUUCAAUACUAAA
GGCUCUAAAAUGAAAAAUAAACAAAUAUAAUAACCAAGCGAAUGAUCCAGGAACCGAACC
AUUGGUUCCGAUAAGUCUCAAAUGACUUCGGGCUAUUACAGGAAGGCUUUACGAUUCAAA
GCACACAUACUCAAACAACAAUAUCAUGCCAAAAUGGACUACCCAAAUUCAUUUAUUAAG
GUUGAGCGCCCAGUUGUUUUUUGCUUCGGCCUUUCCUGUAUGGUAUCUUCCUUUUGUUGU
UUUCACAUAUGCAUCAUAGGCCAUUUCACUUAGUCUUUUCUUGGAGGUUUUACUCGACAG
AAAAUGUGGCUAGCCUAUCAAAAUGCGAUAGAAGAGCCCAAAGACUCGGACGAAUUCAUG
CAAACAAAAAGAAGAAAAGAUUAGCAAUAAAUCCAAGGUCACAAACUUAUAAAAUUAAGA
UAAUCUCAGUCUUAGGAUAAUGCAAUUAAAAGUGUGAGUAAGCAUUAAAGGGGGUAUAUU
ACUUCUCACUUUUCUGUGGCAUGCUCAAAGUGAAAAAAGCUAACACCCAUAGUCAAAUAG
UUAAGAGUACCAGUUAUAUAAAGGAAAACAUAGAAUGCAUAAGGCAGUUGAAUUUUUGGG
CAACUAAUUAGAUCCAAAACACACUAAAUAGGAGAGGCUACACAGAUCAUGACGAACCUU
AAGUGAUUAUCUAUCACCUAUAUCCAGAUAUCAAUCUUGUGGUAUCUCCUAAUACUCAAC
UAUGAACAUGAUUGUUGCAUGCUGAUUUUAACUCCCAAGAUGCUUGGAUUUUUAUUAGAU
AUACAUGGUCACAAAUCCCAAUACAGAGUUGUAAUAAAACAAUCCUAAAUUCUCCAUAAG
AUAACCAAGAAAAUAGGAGAAGAGUUGAACAUUAUAUUUUAAGAGAAACAAAAUGUUCAG
UACACAAUGAGCAAACAAACCUCAAAAUAAACUGGACAUGCUACCGAGAAAAGGGUGUUU
GGCCUAGUCUAGGACAUGUUAUUAUCACUUAAGGAGGAGUCUAUUUAAACAAAAUUGAUU
CUACCAGUCAAUAAGCACUAGCUAGACCAGAAAGGCUUCACCUUUGAGCAUGAAAUAUCA
UCUAAAAGAACUUAACAAUACACUAGUCACCAUUUAUUGAUUUUAACAAACAUUACCUUU
CCAGCUAAACAUGACUACUACAUAUUCAUACUCUUGAUCGAAAAACAACACGGAGACCUU
UAAAUCCAACUUAUUCAAGACUUAAGCAUGUCGGUAUAUACCCUUAAACAAUGAAUACAC
CGGCGACAAUUUGACAUUCAUAAUCCAAGUUCAAGGUAUAAGUAAUGAACAUUUUUGGAG
GGAAAAGGAGGUGCUUAGCCAGCAUGCCUUAUACUGAAAAUAAAACCCAAACUUGAAUAC
ACAAUAACUAACCACCAGUUUCCCUAAAACAGUGGUUAAGCAAACAACACUCCAACAUAU
CGUUAAGAAUUUAUACCAAGAGGUUUUAACUUCAGUUUAUAUUACAUGAUUUACCGCUUU
AUAUUAAUCAGAGAGAAACAAAUCUGUCAAAACCAUCCUAUGUAUAUAUAUAUAUAUAUA
GAAAACAUCAGUCUCGUAUACGUUAAACAAGACUAAAUCUUUAAGGCAUAGUUAUGACAC
ACAUGUAAAAUUUGAAAUCACAUACUCCUAUGUUCUAAUUCCUUCAUGCUCACUUCUUAU
AUUCUCCUAAGUUCAAGUGAUGAGAUCCUUAACGAACAAACCAACAUUUCAUUACUGAUU
UAACCAAGCAAGAAAACAAACAAUGGAAAACAUUUGAUAAAGACUCAAUCUUGGUGAUUA
AAACAAGGUUUACACGAACUUGAUAGGAUGCACACCAUGAAUGGACCCCAAAAACCUACU
CUAAACAUGCUGUCAAACCUUAAAUGAAAGGCUAAUCACACAUAGGCCAGCACACCUAGU
AUAAAGAUUUGGACUUUAAUACAAAAGAAAGAAGAACCCAAUCACUUAGAAAGCAUACCU
AGACUAAAACUAAAACUAACUUUUUACUAUUAAAAUGUUCCAGUUUUAGUUAAAACCACC
UCUUGCAUCUCUAAGGUAGGACACUCUCUAUUCAUACCUCUCAAUCAGGAAACCCCAAAA
GAAUAAAUCUUAAUGCUCAAUCAACCCGUUUAAACAAAUAGGUGAGAGUCUUUAGCUAAA
UUGUGAAACAUAGACAGUUGAAGUCCUUCAAAGCUUAUAUCUUUAUCGCCAUAUGCUUAU
CGUAGAUUUGUAGAACAAACACGUUGAGGAAAAUACUAAUGUCCUGGCAACUAAUUCAAU
AGAAGAACAUGGAUAGGGCACUCCAAAUGUAUUAGUCUUUGUUAAAUAUAGCAGCCGAAC
AAGUAGUAUAUUUAAUGAAUCCAAAACAAUUUCGACUAUCACGCUAAAUAAGUAAGUUGG
UCAUUCUUUUCUAAGUCCAAACUUAAAUUUAAUCUAAAUCACUUACUAAUUACCAGAUUG
UGAAUAGGGGUCCAGCAGGCAACACACUUUACCAGACUACCCAACUCUUUCGUGCAAUUC
CUUAAACUGAAAACAUUUGGCUAUAAGUUGAAACAGUCCAAUUUUAAGAGGGAAUCAAAU
UGAGAAAAUUAGCUUUUACACAUUUACCAUGUUCGAAAUUUAAAGGAGAAGAAACCAUAA
UCAUCCAGUUCUCAGCUAGUGCAAACAGUCAGUCAUUUUUCUCCUAAUCACGAAACUUAU
AGAAAGAAAAACAGAAAGGAAAGAACAAGCAAAUCACCUAUUGAGGCAGCGAACCGAAAC
UUCAAGCCUUCAUCGGAACUCCUCAACGCCACUGGAAACACAAUUUUCUCAACUGAAAUC
CCAAGCUAACUAAGAGUCUUACAAGGAUUUUUACCCUAGAAACUACUGAUAGCCAAACUC
UUUUAUGAUGGGGAUUUCCGCUCAUGAACCAUGCUCAAAAACACUUGUAUUCUUCACAAA
AAUAAAUUACUUUGGGGUUUUUUCUUCUUAUCAGAAUCAUUACCCGCACAAAAUGAAUCG
UAGGGUAUUUAUAGGAGGAAAAGUUGAGGGAUUUGAAAGGGCAAAUCGAUGUGGGAUUUG
GCAAUUUCUAGGUUUUUUGGGAAUUCUCAGAGAUCUCCAUGUAGGAUAAGGUUCCAUAUG
GAUUUCGUACGAAUUCAUACUAAUUGGGAAUGGAUUUCAAAUUGCGAUUUGGUAUUUCUU
AGAGAAAAUGACACUUAGCUUGUCUGGAAACUUUUGGGAGUAGAAAUAUUUUGUUAGGCA
UGCAAGCUCUAUAUGGAAUCGCAGGGAGACGUUGAAGGCAGCGCCGUUUGGAGCUGUUGU
UGCUGCUGGUAGCUUCGUUCGAGAGUACAAGAGCACACAAAGGGUCAUUUGGUGUCGGUG
UGAAGCAGAACCAGAUGAAGUAAAGGGGAAAUCAGG

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 [-778.07] kcal/mol.

2. The frequency of mfe structure in ensemble 4.49415e-47.

3. The ensemble diversity 1058.45.

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