lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-461.00) is given below.

1. Sequence-
CUUUAGUAACAACUGUACUACUAAAACCCACGGAAUGCUCAGUACAAGCUUAUGAAGCAA
UCCCUAACACCAAUAAAAGGAAUUGAUUGGUCGCAUUAACAAUAAUGAUAAUGUGAAACC
ACUGAAACCUAGGAAGUGUGAAUCACAUCAUCAUAACUACCACUCUUAACAGUUCAAAGC
AGGUUAUCGAAGAGAAUAGCAUUAAGUGUUGCAAUCAUCACAUUUUCAGGCAAGGAGACU
GUACCUAGUGUUUGGAAUAAAUAGGAAUACAUAUGCUCUUGAUGUUCAGAAGUGGCUGCU
UGUGAGCUGGAAACCAUGGGCUUUAAUGCAACGAGCGAGCUAUGUCUAAUGGCUUGCGGC
UUGGCUCUCUUUGCUUUAUGUUAAAAUCGGCUGCUCAUCCAGUGUCCUUAUUGAACCAUC
GUUGCAGGCUAUGUUCUACCCUUUUUAUUCCUUGCCGUGUCUCAUCCAAAGAAACCUACA
AUCAUCAGGUUCUACGAGCAAGAACUUUACUUCAGCAGCAAGCCCGCAAGAAACACAACC
ACUCAUUUAGAAUCAUGUCCUAAAAGACGCAUGUUGCAAUAUUGUCCAUGUAUUUUGGGU
UGGUUAGUUAUCUAUCCUUUCUCAAUGUAAGAUCCAGACCACCAAAAGAAUAGGAGAAAA
GAUAUGUAAGAUGCAACCUUUAUCUGGAUUAAGACAAGCACUUUAAUGGUGACAGAUGGC
AGAAAAACAAUAGGUGAAUAAAUUUUGCAAUCACAUCCAGGAAAUAUUAGAAAGAAUCCA
AUAACCAUUUGUCGAGUGUGUGGGACAAUUCUAUAAUAUUAUAAAAGAUCAGGCCUAACG
UGCUAGGCUUAAUAAAGGGCAAAAAAUUACUGUUCAAUGCACUUCAUCCAAAUUCCUUGA
CUCAAUCUUGAGGUGGUGGAAUUAUUCUCUGGGACAAAAAUAUUAAAAACGGAACUGCUA
GGUGAAUGAUGGAACCAUAUGCUAGAAUUAUCAAAGAUGACAAAGUUUUUCACCAUGUAA
AAGGCAUACAUGGCCAAAGGAAAAAGGAAAAGAUGGAUGGCAACUCGAGUAGAUGGCACU
CAUGCACCAAGACAAAUGGCAUAGUCCACAAUCUAGGUCGGACAUAAAGUAUGGAAAACC
AAAUAAACAAGUAAAAAUAAGAAGUCGGUGCAGUCCUUGAGUCACUUUUUCUUUUUCUAU
CCAGUCAUGUAUGUCAUAUUAUCAGAUGGCUUGUCCUUCCCAAUAUCUCAUAAGUAUUUG
CAUGUUUUGUGGUCUUUGGUUCUAUGGGAAUUGGUCUUAGUUAUACUUCUGUCAUAGUUA
CCGGAAAGUUCAUUUCACGAGUUUGAAAUAUGUCGUGCUGAAAAAAAGAAGUUUGAAACA
CAGUAAUGACUGCCUCACAUCAGAGCAGAACUAUAUUUCACAUGAAUAAGGAGAAUUUCG
AGACAAGAACUUCAGGGCCAAUAGUAUAAUAAAAAAGUUGAAAGUUAUGCAUCAUGAGUA
CGACCGCAUUUAUGAGAAUCCACACAAGUCAACCUAAUACAACUUUUUUAAAAGAGACUA
CCAAGCAACUCGAGACUGCAUAUGUGAUAUGUCCACCUUCCAAGACUACAACACAUUCUA
UUGGAAACACUUACAAGAAACUGCUGCAACACAAACUCUACAGGAGGAACAUCAACACAA
GCAAUGAUUUGCGUCAAAACAAUGAUUAGUGGUAAUGAUAACUUACCAACAAUAUUGCCA
CACUAGAAUGAAUCAAUAAUAUUCAAUGUGACAAGAAGAGGUGAAAAUGGAUUAUGGAUG
GAAUGGUAAGUGAUCAUGAACUUAAGUAUUCUUCCCAAUUUUUGUUUCAUAAACCUGAUA
GGUUUGCUUGCCACCAACCAUGGUUGUGCAAGUCAAUAUUGUAAUAGCUGCUCCGCUAAC
UAUUAUUCUAGAACUUAAGCUGCAAACAAUGUAAGAUGAUACUGUAUUUUCUAUCAAAAG
AAGUUCCCAUCAUCAAUAAAUUAAUAACCUUCCCUGCACAUCACCUAAACCAGCCUAUUA
GAAGUUAUCUUUUAUUAUCACCUUGCAUGUUUUCAUGUGGAAGGUUUUUUUUUU

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 [-498.34] kcal/mol.

2. The frequency of mfe structure in ensemble 4.85375e-27.

3. The ensemble diversity 395.43.

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