lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-462.89) is given below.

1. Sequence-
UAGGUGAGUAAAACUAAUGGAGCAUAAAACUGCAUAUACAAUGUGAUCUUGCAAGGAAAC
AUGCAGUCAACUCUCAGUUCCACAUUUACUUAAAUAAUUAUAGCGAUGCCAUUUGAAGUA
AUGAAGUAAGACACUCAAUAUUCUAAAUUGUCCAAGAAUAAGCAUUUUCAAGGAGAACCC
CUAAGAGGCAGGGGGUAUUAACAACAUGUUAGCAUAUUAAACUUAACCAAGACUUAGUAA
AUAGACAUGGAACAACCCUGUUUUAGCUACAUAUACAUGUUUUUAUUACCAAUAUCAAGU
AGAAGUAACCAUCACCUUAUUUACUAAUUAAAGUUCCCAAAUUAACUUAACCUUGCAUGA
UUAACAAUUUGAAGAGCUAGCAGCAACAAAUGGACCUAUAAAUACCCUAAUGACCUCAUU
UAGAAAGACCAGCUGUUAAAUCAAGUCCAUUCCCACAUAUGGAUGCCAUCUAGCAUGCAA
AGUACUUUAUUUAGGCUGAACAUGCAUAACUACCCUUAUCAAUGAGUCAUGACUCACGAC
UUUCCAAUGCUCAUUCAAACACCUUAAAAUCUCAAAAAAGAAUAAACAUUUCAUAUCUUU
GAAAUAGUAGGGCUCCUCUAGUAUGUUGAACAGUCAGUUAAAGCAAAAUCAAGCAACAAA
CAACCCUUUAGCAAGCAACACUCCUAUUUAAAUAUACACAUUAAAAGCAGCCUAUGAAGA
AACUUUCACUUUCAAGAACAAGGUAGAUAGUUUUCCUCCCCAUGAGUCAUGUUCAUGUUA
UGCAUUUUAGACAGAAAACAACCAGCAACUAAUUUAUACUGUAAAAGAAAAAACAAACUA
AUUGACAUAAAAACAUGAGAAGGCUAUGGCAGUAGACCCCCUCCCUCUAAGAUGAGCUAA
ACUCAACCAAAAGUUGGUUCAUUUCCCCCAAGACUAACAUACAGAGAGCACACAGUUAUA
UUUCACCUAAAAGAUUCUAACUUUACACCUGAUACCAUCAAAUUAGAGGUGAUUGAAUCC
UAAAUAUGAUGCUAGGUUGGUUUAUCAGAAGAAGACUCAAAGACUUCAACUUUUGAGACA
AAAGAAUAGCCAAGUUAUGCAUGAUAGAAAACUUGAGAUAAAAAAAUAAACAUUGAAGCA
CAAAUGGAAACCUAAAUAAACUGCCGCAUCUGAUUUUAAGAUUUUAGAACCACCUGGCUG
GCAGUAGAUAGAACCCUCCCAAACUUACUAUGAGCACCUCAUUUACAAAUCUGACUAAAA
AGACCUAGAAAACAAGAAUGCACAUAGUAUCUUGUUGAAUGAACCAAAGAAGGUAAAAAG
GAAAGGUAACACAAGAGAAAGCAUAGCCAGUACAUAGUAAACUAAGAGACUUAUAUGCCC
UCUAUAUGUCAAACAACCUUCAGAUAACACUUGAAACCAAAAGACAUGUUCAAUAUUUAA
CCUAAUGUAACAUUGAGUUUAUGUGAAGCUAAACAUAAUGUCGAGGCAUGUGAGCACACA
CAUAUAUGCAGCCAGGUGGUCAUAGAGACUAUUUUUAGCAUAAAAUGCAUAGAACAUACA
AAUUUCAAAUUGAACAGCUUUAAGGUCUUGUUAAGUUAUAUGAACAAUCUCGCAGAAAGG
AUUCCUGGGGAUAAUCUAAAACAUAUUUGAGGUCAGGAUUGAAAGAUGAGCCAUACAUAA
CAAAACUAGAUAGUUCAAUUCAUAAAGGUCCAAAAUUUGACACAGUUUUUACACAACAAA
AAACCCAGGUCAAAACAUGACAUUACCAACAAAUUUUACCCCUUAGAAUGUUGUAUAGUG
ACCUGAACAUGGAAAUACCUCAUUAUAGAGCACAUGAAGCUUAUUUAUAAGCUUAAGAAC
AACAAAUCACUCAUUGAAUUUUAGACAUAAAAUAGCCUUAAAGGCUCCAACUUUAAACCU
AAAUGAGUAAAAAUUGCAACCAGCAUUUAAACAGGUCCCUCUUUUCUCCUAUACUAUGCC
AUACACCAGAACUCCUUAGUCAAAUCAACACAUAACUCUCAAUAGCGCUUCAAGACAGUA
AAGGAACUUCAGCAAAGCAAGUAGCCAAACAACUUAAUCUUACUCAGUAAAGAUUUAAAG
CCCAUUACUAGAUCAUCAAAGAACCUAAAUCAGAAUAUUUUACUUCUGUUUUGAGUCCAU
UAUCAAGCCUUAACCUCCAUGAAUGACAUAUACACCUUUCUAAAACUUUAAAACAAAAAC
CAACAAAGUCAUACCAAGUCAUAAACAUCAAAGUGCUAAGCUUCGUUUUUAACAUAGAUG
AAUUCAUUUAGUGAAUUAUUGAGCUAAACACCACACAAGAAGACUAAUACUCACACUGGA
ACAGAAAAAUACAUGUUCAAAACUCAAUUAUUUAACCAAAAUGUUAAGAAAAUAAGACAG
AAUAUAGGGUUUUUACCUAGUUUGGGCAGGAAGCUUGGACGUUAACAAGUUGAAGUGAUU
CUUCACUACCUUGAGCCUUGAUUUCAGCUCUUUUAAGCUUC

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 [-506.88] kcal/mol.

2. The frequency of mfe structure in ensemble 9.97357e-32.

3. The ensemble diversity 483.15.

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