lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-594.40) is given below.

1. Sequence-
CCUUAACUACUUAUUUGUGAUAAAUAGUGUUUUUUUUUCUUUCUUAUUAUGUGGUUUUCC
UUAGCUAUUUCCUACAACCAUGGUAGGUUCGACUUGCUUUUGUAGCAUAGCUUGCUUUGA
UUUAGCCCUAACCUUAGUCUAUAAAGGGUUUUGGAGGUGGUUCUAGUAUGAUGUCUCUGA
AUUUACUGCAUAUGAUAUGUAUGACACUGUUUUCCUGUGAUAAUUUGAGUAAUACUGUUG
CUUCUUGAUCAUCUUGGCUGGUUCUAGUUCUUAGCUUUCUUGCUUGUUGAGGUUAAGUGU
UUGAACUUGAUGGAUGUUAAUGGUUAGUGUUGCUUCUAUGGUAAUCUUAGGUAAAUAUGU
UGUGUUCUUUUGAUUAUGUCCACUGAUCUAGUUGUGCUCCUAUUUUUUGGUGUUAGUUAG
UUCUUAAUAGUUGAGUAAAUGAUUUCUUUCUUAUUGAUAGUAUAUGCAAGAACCUACUAC
AUGAUGUAUGAUUGAAAUUGUUUCUGGGGUAACUUUGAACCUCAAAAAAUGGUGUUUCUU
GAUUCUGUCUGGUCAUGCGAUUAUUUUUAGUAGCUUUUAAAAGUUUGAAACAAGUUCUGA
UUCAUGCCUUUUUGUUAUGUGUUCUUCUGUUGAAAUCUGUGACUACAUGUUAGACUGUUU
UCCUAUGUUUUUCCCCUUUUAACUGAUUUUCAUUCAUACUUUACCCCUAAAGUUUUAUGC
AAACUCUUUUUAAACUAAGGGAUAAAAGUAUCUAAGGUUUCCUAUUGAUGAGUAGGGUAA
UGGAGGCGGUCUUAAUUCCAUUUAAUCCCUUGUUUUCAAGAUGAUACAUAUAGGGUCUCU
ACUAGUCCAUGUAUUCUUUGAUUUCGUUCCCCCUGUAAGAUAAAUAUUACAACCUAUGAG
GUCUGCAAGUUUCACAUUUGAAAUGAUCAUCUUGACACCCUAAAAUCAUAAAGCAAAACC
CCAUUAGUCCACCCCAUACUCUGAUUUUCAAGGUUGUCCCUAUGUGAUCCCUUAUUUGCA
AAGUAACCUUCUUAGAGUUUUGUUUUCAGUUUCAAAAGGGCUUUAAGGGAAGUGAAGGGC
UUAGUACUUAUUCAUUUCAUCCCUUCUUUACCUAAACUGCACAAGGACCUGUAUGAGUAC
AAGGCAAGGAGAAGGCUUGUGAGAUGGAACUUGGGAAUUGAAUAUUUGUUUUGCCUAUCC
UAAGAACCUAUACCUUGUAAUGAUGCCUAAAGUGAGGGGUGUGGGUCGAUAUGGGGUUCA
ACUCACCUCUAAUGAGUUCAAGGGUAUAAUUAUCUAAAAGGCUGAGGGAUAGAGGACAUU
UAAAUGUCCUCUCCACUGCUUUUGAAGUGAUUUUCAAACUCAAAAAUAUCUUUAUGAAGU
CUUGGCCAUUUUUUCUAUUUUCUAGUUUUAUUGAAGUCAAUAUUGCUUUUCAGUUUUUAG
UUAACUGCUUUAAUGGUAUCAUGUCAUGUUAUUUUUGUAUCUAUGUGACUGGUCGGCAAC
AUUCUUAGGUGUAUUCUGGUUGAUCCUUUCAUAAUGCUGACUUGAUGAAACUAGAAAUGU
UUUUGUGUAUUUUUAAGCUUUUUGAAUCAUGCAUUCACUGGUUAUAUGUUGCUUCUGUAG
UUAGGAGGUCUGAAAUGAUUUCCAUGCUCUAAUGUGAAAUAGUUUGUAAGUGUAACUAGC
CUAUAUGCCUUCCUCCAUUGAAAAGCUUGCUGCAUGCUCAUUCUUGCUAAACUAAUUGAG
UAAAAUUGGAGUUUUUCCUUCCAUGAUCACUAGUAUGAUCUUCACAAUUUAAUAAGACUA
UUUUCCUGGAUUUCUUAAAUUUGGACUGAAAACUGAUAAUACCAAGUCUGUACACUGUGU
GCAUAACCUGCCCUGUUCCAGUUGUAUUUAUACUGUCUAUUUGCUUUGUUUGAGUAUAUU
AUUUGGUUUUUGUGUUUUCUAUGCAUGUACCCUCUCAUGUUAGCUAGCUAACUGCUUAAC
AAGAGCUUAUUUGAUCCUACAUAGUCUUCCUACUGCCUGCUAACUUGUUAAGGUUUAUUG
GUAGUUUAAUACCUGCGCAUCUAUAUGUUAUUGGUUAAGUUCAAAUGUUUUUUCAUGUGA
GUUAAAGUAGACUGCUUAAGAGACAUAUAUCAUGCCUAGAAUGUGUUUUGUGACUCGAGG
GCCAGUCUAACAUGCUCAGUAUACUCCCUUCCCUUGAGACUAUCAUGAUGUCUACAUAUU
UUCCUUUUUUUUUGAAGUUGUGUGCAUGAACCUCUCUAUUCUCUUGUCUAACUGAUUCUA
UAUGCAAGACUUGAUCAAGGGUGUGUUCGGUAUGAGGGAAAAUAUUUUUUGAAAAAUGUU
UUCCUAUUUUCCUAUAUUCGUUUGGUUAAUAAUUUUGAAAAUACUUUUCCUAGGAAAACA
ACUUCCUUGAAAAUAAGCAAAAUGACUUUCAAAAUAAAAAUAGGGAAAAACACUUUGGAG
UGAACACCCAUCCGAACAAGUAGGGUCAAUAGUUCAGCAUUUAAGCUGUAACAUAAGUUC
CAAACUUUUCUACCACCUUCAAAACUAUCCCACCUUCACCCCUACCCCAAACCACUCCCU
CUACCUUGACCCCUCAACCCAC

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 [-641.88] kcal/mol.

2. The frequency of mfe structure in ensemble 3.4762e-34.

3. The ensemble diversity 715.47.

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