lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-456.00) is given below.

1. Sequence-
GUUGAAAGUUAGUGAAUAUGUUGAAAAUUACUCCUUUUACAGCCUCAAAAACGUACACAU
AUUUAGCCUAACAUGAUGUUUUAACAAUAUUAAAUUAGUACCAAAGCUUUACAUUGUAUU
UAUAACGUUUUUGAACCCUUAGGAACACCUGUGCAUCGCGUGGCAUAUGUGAUGAGUUAA
UCGGCACGUUGCGGACUUGUGGAACUCUAAAUCAGUAUCUCUUUGUAUUAAGGGGCAUGC
AUCCCAUGGUGAAAUAAAGUUAUUCCCAUGCAGGUUGCUUCUCAGAAACAGUUCACUCAC
AACUGUGCACUUCUAGCUUCCUGUCCGACUUUGGGUGUCUGUCUACUGCUUUAUUUCGUU
CUUGUAAGCUCCUAGAUUUGUCAAUUUGUCAACAUGGGUCUAGUAUAUUCACUACCAAGC
UGUAAAAAAGUCCCAACUACUCACCACUUGAUAACCACAAAGCUACCAAAAGCUAGAGGA
ACCACUGGGCACCAUGUCGGCUAGGCAUCUCGUCAUGAGUUUUCCUUGCGAAUUCUCUUC
AUUUUGAGCUUCUAUAUUGAUUCUUACUUCUUGAUAACUUAUAAUAGGUUGCAACUGGUU
UCCAAAUAAGUUUCCAAACCUCCAGUUUUAAGCCUCACAAGCACUCCAUGACAGCUUCAA
AGUUGGUUGGCAACUAAGCUUAACUAGUCUUGACUAGUUUUGCUUGGGAGUUUUGCUCCU
UAUUUCCUUCAUUUCAAUGUAACUUGUAAAUAAGCACCAAAAUCACCCUACACAAUCUCA
UACAAAUUAUUAGGUUAUUCAACACAUCAAACUCAAAAAAAACACUAAAGCAUGCCUAGA
UUAGCUGGUUUAAACUAAUAAUCUGGUCAAACCUUUAUCUUUUCAUUUUUGCACUUGUUU
UGGACCAAUUGAAUCACAAACAACCCAUCAAGGUACUUAGUACAUAUUUACACCAAUUUU
AAUAUUUAUCCUUGCAAACACUCUAAGUUAUCCUCAAAAUAAAGCUAAAAGGUGGGUAGA
AUAAGAAAAACAAGUGUGUACUUGCACCUACUAUCAUACAACUCUCCCUUCAUAACUCUU
AAAAUUCUUCUUUAUCUAAUAGCUUAGACACCAUUUUACUUAUUUAUAUAGGGCCAUCAU
AAUUACCAAUCUCAUGUUUAACAUAUUCACACCUAUUGUAAGUAAUAAAUCUAAUCUUUU
UUUAUUUAUUGUAUCAAGCUUACUAGAGAAACUUUACAUGCCAACAUUACUAUCUCUUCA
AACUAUCAUUGUUUCUUUACCACAGUGAUCAUCUAGAGUUCAAACUUAGUGUUCAAUACU
AAAAUUGGGUAUAACACAAGUUACUCUUACUGCUUAAUCUUCAAGGUUAUUUUAUUACCA
UUCAAGGUAACACUACACCUUUGAGACACAACAACAAAAAAAUCAUAAUCUUAAUCAUGC
ACCGUAUCUAGUCAUAGCCUACACACACCUUUAUUUUUCACCACCUCAUUAAAAUCAAUU
CAUUCCCUAUAGCUCUUGUAUCUAUACUAACUUCAUAACCUUAUGAAUACUAUAGAUUCU
CUCGUAAAAACCACAAAGAAAAAUCUAAAUCCAUAAAUUACCUUAUAUUUUACUUGCAUU
CUAUACUUGAUCUUCCUAACAAAAUAACUUGAAAUCAUAAACUCCUUUCCUAAUCCAAAU
ACAACUAAGUCAUGUUAACUAACAAUUCCUCUAAAUUCCUACAUAUAGCCUAUACCUACU
UAAUGCACCUUAGUCAAUAUUUAAUGACAUCACCUGAUUACUCACUUAAUAACCACACGG
UUAUAACUACAUACAUCAAUCAAUAACUAGGUCCAUAUUCGACCUCGUACACUUCAAACU
UCAAACACCUAACUGUGGUUGUUUUAGUACUUAUCGCUCAUAGCAUCUCAAGUCUCAAUA
CCUGUUGGGUGACAACACUAGUCAUUUGUUCUAAGACAUGCUUCCCCUUUAAUGGUCUCA
UCUGUGGUAAAGACAAACAAACCAUUUUUAAGCCUAAACAUAGCUGUUGUAUACCAAUUU
AGCAAGUCAACUCUUCAAUUUAAAUAAGCAUAUUUACGUACUCAUACCACUGUAAAGGCA
UGGCUUCUAUACAUGCAAACAUACAUGCUGAAACAGUCCCAGUCAACUAAUUAUUUCAUG
CUUCAUUACCAAAAAAUUAAAUAAAAGGAAAGGCCAAAUAAGCCAUUAAGAUGGCAGGAA
GCUACUCCCAACAAAGAACCCAUCAGUACAAGACAUUGAAAUUGUAGCUUUAGAAUGAAA
GGUUUGUAUAUACUAAACUAUCCAGAUCUUAACAUUCUUCCAAACACCCUUUUAAAUCAA
UCUCUUAUUUUACCUAGAACACACUAGCAUACCAAGCAGUGACUUAAACCAAGCAGCACA
UAAAGCUCAACAAUAAUGCCCCAUAGAUCUUCAAAUAGCUGCAUAUAUUGACCACUAAAC
CACCAAGGAUAGUUUUUGUUCAUGGAUGAAGCAAUGACCUUAAUAGGCUAAUCAAGAAUA
AAAUUUAAGACACUAGAUCAACAAAACACAGACCUCAUGCUUUAGAUAAUAACCUUCCCC
AAUAAAUAAUAAGAAGCAGGCAUGCUGUCUCAUGUUGACUGACCUCAAGACAUGAACCCC
AGCAGUAAAACAACCCAAACAGUCAAGUAAAU

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 [-501.13] kcal/mol.

2. The frequency of mfe structure in ensemble 1.59314e-32.

3. The ensemble diversity 748.94.

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