lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-455.10) is given below.

1. Sequence-
UUUGUUAAAGGUAGUGUCCAGCUGUUCUAAGGCCAUUUCUUGCUUGUUGAUGUAACAAAG
AUGGCUUCAAAUGCCUGUAAACACACAAAUUCAAGGAUCUCAGAACAAAGAAAAACAAGA
CUUGAAGUUCAUCAUAAACACUAAGAAAAAUGGGAACCUUAAGGAAAUACUAUUGAUCUU
CUUCUCAAGGUACACUGCAUAAUAAAUCACAAGGAUGGUCCCAAACAACUCAAAGAGCAU
CGACAAAAUAAAAGGCGUUACGUGAAAAAACUAAAUGUACUAGACUUACUAGUAAAUUAC
AAGAGAAUAGGCCCCAUUAAUAUGGAUUAGAUAAAGAACAAAACAAGUCCAAUAUGUGGU
ACAGGUUGAGUACAAGGAGAAACCACCUAUUGGUUUUGCCAAAAGCCAUAUCCAACAGCU
AUCACAAAAUUCCAAGCAUUGUACGAGGACAAAUCAGUUUUUCCAAGGAUAAGAACAACU
ACAUGAAAAUGAAAUUGAUGCCUAGAUGGUAAAUAAAGAGAUGGAACGCCAUAGGCAUUU
AAUAAAAAUCUGAAUAGAGGUUUUAGAAUAUGUGUCUCUGCUCAACUUAUCCAACUAACA
AGUCAAUUCAAAUUUAAUAGGUAAACCACAUUGGAAUAAAGCUUCAUUAUCACAGAAAAU
AAACCAAUAAAUCAUGAAAGCAAAGUACUGUAUUUACUAUGGAAAACCACAACAUUAAUC
AUUAAAAGAAUCGAUGUUGUUGUCCACAGACUCAAAAAAAAAUAUUGGUUGCUGAGGAAU
AGCUUCGUGGCUUAAUAUGGUUCUACCAAAAUUAAUUUAAUUUAACAUGAUCUAUGCGAU
GAGGAUUCACAACUAGAGUCAGAUAUAUCUGUGAUAGCUACGGUUUGUAAUAACAUUUCA
UUACAAUAGCCAAGUUUCUUUGGAAACGAUUUGUUUACGUCUCACAUCAAAAUUUCAACA
GUAAGGCCAAUUCAAUUUUCCAGUCUUUCCUUCAAAAUCUUAAUAGUAAAGUGCCCUGCU
UACAUAAGGAUCCCAAGAAUUGGGAAAAUUGAGGAUCCAUAACUUAACAAAAAGUAUAAG
AGAGACUAGUAUUACCACUUUUUUUUCAAGUUAAACAAUGAUAGAUGGCUUAAAAAACAG
AAUCCAUUGAACUAAUUUUAGGCAAUUACGUUCCGACUCAUCAAAAAUAUUGUCAGGUGC
AUGUCGGAUCCUUCAAAUUAGUUUAUUUCUAAGGAUCCAACACGAAUGCGACAACUCUUU
UGAAGUGUCCGAGCAACAUACGUUUUAGGUAAUUUUCAAAGGAACUACAAGUAUCAAGAA
ACUCCUGAGCUGCAGAUUUAAAGAAAGAUAUUCCGGAACAUGUUAAAAAUGUUAAUUCUG
GUGAUUUUCUUUUUUCCCUUUCUACCCACAACCCCAUAAAGGAACAACGUUUUGUCCCUA
AAACUAUAAAACAGAACAACCUAGCUAUAUCCAAAACAGACAUUGGUAUGGGGUGAAGAG
AAGGAAUUAGAAUGUUUUAGUCCUACAUGGUGGCGGAUCCAGAGGCAUAACAAACAUAGC
AAGUAAACUCAGGAAGAAGUUAAAAGGAGAUUAAAUCUUUACUAUAUAUAUAUACAGUAA
AUGAUUUUUUAACCUUGGGACAGUUUUAGCAACCCCUUGCAUCCCCCAGCUCUACUUCUA
GCCUACACAACCAAAUUUACCAUUCCAAACUUAUAUUUCUAAACAAACCUUUUAUUUGUU
CAAGAAAGUUAAUUUCACGUUCAUCAAAAUUCACAGUCAAUCCCCAAAAAAUCCCAUCGA
AUCAAACGACCACCACUCCAGCACACGAAUCAGAAUUUUGAUUAAGAGGUUCAAAAUAUA
AAAAAGUAAACAUAAGAAAAGACCAAUAUCUACUAUAUAUGUAUUAAAAAUAAUAAUUUU
AAUCAUAUAUAAACACCGUAAUUUUCUGUCAAUUCUAUCUAACUCUGCCCCUGCCACCAC
CCACCCCAAAGGAAAGAUGAAAAAACGACAAACCCCAUUAAGAAAAAUGCAACAACAUGA
UGCUUAAGGCACAGAGUACUUCAAAAUAUAAAGAUCUAAACUUUUCUAUCCAUUCUCAAC
AAUAAAAAUCUGCACUUCACCUCAAACAUAAGAGGAUGCGGUGUGUGUGUGGUGGCUACC
AAGCUAUAUGAAUAACACUUAAGGAAACAGAUAGAGAGAGACUUAAAUAAUGAAAAAAGA
AACAUACCCAAAUAGUAUAAUUGUAUCAAGAAGGUUUGUGAACUAAGAUACAAGUAAAAG
AUUGAGUCUUUAGAGAGAGAAAGCAAAGAAUCCUUUUGUGUUUAUAAGCAAAGGUGAAAA
ACAGAGUAGAUGGGUUGAAUGUUUUGGUUCUCUAUAUAUACACCCAGUUUUAAGAAGAC

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 [-497.32] kcal/mol.

2. The frequency of mfe structure in ensemble 1.77461e-30.

3. The ensemble diversity 473.97.

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