lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-417.19) is given below.

1. Sequence-
CCUUGGCCCCCACUAGAUUCCACACAACAUAGAAAAAUACAAAUAUAAGAAAAUACAUAA
GAAAAAGGAAAAACAAACUAUAACUUCAAUUGGACCGAUUCCAAUCUUCCAACCUUGGGU
CAUAGCCUCAUGCAAGGAAUCCAGUUUUACACAUGUAAAGAAAGAAAAAAAAUUUGAGUC
GAUGAUAAAUAAGUAAUACAAGUAAAUAACUAAACAACGCAAACAAAUAAAAACAGAAAA
AAACCAUAAUGUCAUCUUAUAUUCGCUAGGCCCCAAAUACACAUAGUUCUAGAAUAUAAC
ACAUGAAUGACCCAAAAUAAAUAAGCUCAAUUAAUUAAUAGGCUAUGAUUAAAGAUAUCU
CCCAUUUAAAUUCAAAGCAUAUCUAGGUCCAGUUAACUUGUACAAUCCAUCCCAAUUUCA
UGAAAUCAAUACAAAAUAGCCAAGUAAAUAAUCAAAUGGCACACUUAGCAUGCACUAUUC
GACCUUAGCAUACAAGGGUUCUAAUAAUUAACACCUUUAUUAAACCUUAAUAGUCUAGGU
GAUACACAAAGUAUGAACAUAGAGACAUUAUGAAGAAAUGAAAUAAGAAAAGUAUAAGGA
CUUUAGCAUUUAUGAACCUCGAGAUUAACCCUAUGACAAUCUAUUUGAGAAAUAUUAAUA
AGAGAAAAAUAAAUAAUGUAUGUUGAUCAACUUAAGCAAUAUGCAUAUAAAAUACAUAAA
CACAUUAUUUAGAAUAUUAUUUAACUUUAAUUAGAAUGAUCAUCUAGUUGAAGUGAUAAU
AAUCCUAUACUAAUAAAAUGUAGAUAAGAGGGUUGUACCUGGAUUUAGUCUCAGGCUAGG
GAAGGGUAAGGCAGAUGUAUAGCUUAUAUGCAAGGAUUAAGCACAGUUAGCAAGUAAGAG
GAGGUAGCAUGUUUCAUAGAAGACCAUAUAAACUUAGCUCAAAGAAGAAACAUACAUCAA
UUUGUAGAAGACAUAUGAACUCAGGUCAAGAGGAGAAGCAUAAGCAAGACUACGAUAUAC
CAUAAACUCAACACAAAGGGAAAGGGGAUGAGGAACAAGAGGUGGGAAAUAGAUUCAUAU
AAGAAGGGAUGAACUCAAAGCGAAUGGGAAGCAACUACCAGUUUAUUUAGUUAACUUAGC
CUAUCAAGCAUAUAAUAUUCAUGGUGAAUAAAUGUAAACAUGUGAACAAGUAACAUGUAG
AUUUAACACAUAUCAAAUCAUGCAUGACAUCUCGGAUUCCAACAUAGAAUAUGACUUAGC
AUGGGGUCAGUAAAGAUAGUCUAAUAAACCUUAAGAUACUGCUUAUUGACUACUUAAUUU
CUAGUUUCAAUUUCAAGUUAAGAAUAAGAAAAAAUUAACAAUAAAGAAAUUUACAUUCAC
UACUCAACAAGUCACAAAACACAAAGAAACAGGUUACAACACUAUUAAGGAAAUUAUUCA
GGAUCACACGUAAGUAUAAGAGUACAACACAUAGAAAAUAAAGUCAGGACUUCAAAUAGG
AGAAUUUUAACCUUUAUUUAACAUAGAGAAAAAAAAUAGUCGGGAGGAUAUUUAAAUAUC
CUUUGUCUCUCAGCCUUUUGGAAAAUCAUACACUUGGACUCCUUAGAGAUUCAACUCAUA
CUUCUCACCUCUGGCAUCCUUGUAGAAUAGGUUCUUAACAUAUGGAAAUAAGUAUCCAAU
UUCCUAAGUUCCAUGUCACAAGUAUUCUUUUUGUCUUGCACUCUAAAAGGUAAUUGUGCA
UUUUCAGUAAAGGAGGUAAAAAGUGAACAAGAUUAAGCCUUUGACUUCUCUUUAAAGCCU
UUUGAAACUGAAAAUGGCUCCACAAACACACUUAACAUAUAAGAGAUCACACAAGGACAG
CUUUAGAAAUUAGAGUAUGUGGUUAGAUAAGGGGGUUUUAUUCUAUGAUAUUUGGGUGUC
AGGGUGAUCCCUUUAAGAUCACUAUAAAGACAAAGGGAGUCAAAUGGCACUAUGAAGGCC
UCAUCUUACCCUACUCAUCAAAUAGGCAACCUUUAAUACCUUAGCCUUUGUUUUGAAAUC
AAGAUUUUAUGAAAGAAGGUUUACGGGUUAAGGGUAUGUGUAAAAACCAUUUUUGAAAAG
AAAGAAAGCAAAGAAAAUAGUCAACACCUAAAAAAAAUAUCAAAACACAACUCAAUUUGA
AAUUGUUAAAGAGUGUUGGAAAUAGAGAGCAUGACCAGUCAAGCAAGCAAUAACAUUUUU
AGUUUAAAAUCAUCUAAAAGAAGCAGUAACAAGUCACACUCAAAAAGAUCAAGAAACCUU
AUUAUUAAGCAUAAAAAUCAACUUAUCCACCUAACAUAGAAAACAUAACUAAGAGAAUAA
AAAACAAGACUUUACUCAAACAAACAAGAGAACAAUACAUAUCAUUCAGCACAUAGAAAG
UUCAAAAUUAUCAAAACCAUCUUCUAAAUCCCCUAUUAACUAGAGUUAGUGAUAAAUCAA
AAUAGG

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 [-462.84] kcal/mol.

2. The frequency of mfe structure in ensemble 6.78251e-33.

3. The ensemble diversity 536.06.

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