lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-626.80) is given below.

1. Sequence-
UUUUUUUUGAGAAGGCAAUAAGGGAUACAUUUAUACAAUAGUUGCAAAAUGAAUUCUGGA
UAGUUCGCAUAACAAAUUAGACAAGAAAAUAAAGUAUAUAAUCCUUCCUCUUUCCUUAUA
CAAGAAUACAAGGUGGUAGUAGACUAAAAAAGAAGCUCAAGAGACAUAAAAUAAGAGUUC
CAGCUUACUCAAAACUAUGAGAAGCCUUGGGCCUGAAGUUUUAAUUCUUGCCCACACACU
CACUCCCUUCUUUCUUCCUUUAUUUGGUCCAACAACACACUGACUAUUCUUGCAAAGACA
GCAUAAGGCUUAAGUAUGAUACCAUAAUCUGUCACACAUCCACAUUAUAUCGAAUAGUCA
CUAGAAUCUUUGUGUCAAUAUUCUUCUCUGGAUCUUAGCUUUGUCCAAGGUCAAUGUACU
GUGUUGCACUCUAUAACCUGCAUCAAGAAAUUCUUUUAAGGAAUGGUCUCUAUGAUGGAA
ACCAAUCUUAUCAUCUACUUCUGUCGUCUCAUCACAAUGUAAUGUACUCGCUAAAGAAUG
GAAAAGAAGUAUAAACAAGACCAACUUGAAAAAGUGAGCCAAAAUUGAAGUUUGAAGUUG
UUCAGACAGUUUAGUUUAGGGAUAACUUCUAUAUAGAACUGGCACACUUGAAAUGUGAUA
GGGCGAUUGGUUUCGUAAAGUAAGAUGAUUUAGUAUGUCGGAUACAUAAUUAAAAAAGUA
AAUGUGAACUCUCCCUAAUAGCUUAAGCUUUUUGACGAGAUAGUCACAAACUUUUAACUC
CAUAUCAGAUCUUUCAAAUUAGUUUCAUGGUCUCUGUGAUAUCCUAUAAGAAAUUUUGAA
UCCUUCAAACUUUUUGGGAUCCGAAAAGUAUUGAAAGAAGUCAAAGUUGUCGAAAGGAUA
UUGCACUCUCUAAGUAUGAAGUUCCACACCAAGAAGACAAUGCUUAAGAGCAUGUUUAGA
UUGGCUUAUUUUAGGUGUUUUAAAGCCAAGAUUGAAUUUAAACACUUUUUUGUAGUGUGA
GUAAAUCUUUUGAAAAAGUGCUUUUAAACACUUGUUUUUAAGUCAAAAUAACAAAAAUAA
GCCAAAAGCCAUAAGUAUGUGUUGGGUUUGGGCUCACUUCCUAUGUGGAGGCCCAAAUAA
AGCCCACUAUUACAAGCUCAUGUUUUGAUAAAAUUAGGAGUUUACAGCAGCCGAAAAACU
GGGAGGAAAAAUAGAGCGUGUGAGCCAGAAAAUCGUGAGAGGAAGAAGGUGCUGUUCACU
UUCGGAUUUCUGCUUGCAGUAUAUUUCGAGCUGGUGUUUGGAGGGUCAAACAGUGCCCAA
UUGUUCUGAAAUUUUGCAGGCAGGUUCGGGACACAUUGAACUUGAUUUCUACUGGUCAGU
UUUUGAUUUGGAGAUCUGUAGGCAGAGAUAUUCGUGUAUGAACAGAGGUCCUGUUUUCUG
AAAUUUUCUGCGUUUUCUCUAGUUGCUUGCUUCUUUGUUGUGGUUGUUGGAGAGAAGCUA
UUUGCAGUAUUAUUGUACUAUUUCAGCCCUUGUUUGACUCUCUCUUGUAACCUGAUUUUG
AUCAUAGUGGAGCUUGUUUGAUGGUUCUUGUGACCCGUGGUUUUUACUCUCUAUUUUUUG
AAGGGAUUUCCACGUAAAAUCUGGUGCCUUUGUUUCUUGUAACUACUGUUUUAUUUGCUG
UUUUUGAUCCUCUUACUCUUGCAAGUGGGGAAUUUGUAUUGUGUUGGUAAAUUUCCAUCA
GUAUGCUUCUAAGUCAUAAGCUAUAAGACCAUCCAAACAGGCUCUAAGACUACCAAGGUU
CUUAACACCUUGGGACUAGAUGAUCCAGAAGGUGAAUUGGUGACACAUGAGAUGUUCUUA
AAUCAACAGAAAAAUGACGCAUUGGUUUUGCCAAUUAUUCAUCGGAUGACUAGAAUGAAU
GAUUUGGUAAAGAAUUGUGCCUUUUUGAAAGAGGUUGGUGUUUUACUAGAAAGAAAUGUU
UGAAGGUCAAGAUGGACUGGUAAUGAAAGAAGUUGGAUUCAUCAAGAAAAAGUUUUUCAU
GUUUUAUGGCAGAAAUGGUUGAUCAAGGUCCAGAAUCAUCAUACAAGUACAUAAUUAUGG
AUAUUGAAAAUGCAAUCAAUUUCGAGCCUCUGCCCAAGAAUUUAUGUGUUGAGAGAACAA
CAAAUUGUUUGCUAGUGAUACAACUGUACCACCUAGAGAAAGGCAAAAGGAUUCAAACAA
AUGUACACGACCAAAUACAAAUCCACUGUACAAAGAAGAUUACUUUAAGGCAAACCUAGU
UAAAUGAUAUCAAGCAGAAACAAAAGUAUGUCGAUGAUAUUUUGAAGAGAUUUAACUUGA
CCCCAAUUGAUGAGAAACUAAAAUUGUCUAAGCAUGAAGUGAUGACUUUGUUGAUGCUAC
AUAUUUUAGGAAAUUAGUGGAGAGUCUAAUUAAGGUACUUGAUUUCUACAAAACCUUAUA
UUAUGUAUAACAGGCUCAAAUUUGAAGAUCUGGGUUUUGAGAGAGACAGUAUUGGAAAUA
AACUAAGAUUAAUUACCUAAAUUAAUUUGAAUUUGGUACUUGUUACUUUCUUUAGUUCAU

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 [-677.46] kcal/mol.

2. The frequency of mfe structure in ensemble 1.99653e-36.

3. The ensemble diversity 520.03.

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