lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-500.70) is given below.

1. Sequence-
CCAAGUUUCAAAAAUCUUUUAUAGCUACAAGCUAAACAAGUAUACACAUAAGAAAACAAU
AAUUUGAAAGAGAGGAGGAAAGUAAAGAGAGAACUUUGGGCCCCAAACACUUAGACCCGA
UUCUCCAAUCUAUACGCCUGGAAGAGAAUCGGAUCUGUCCAUUUAUGGGCCUGUCCUAAG
UCUAGCAAGAUUGGGCUUUCAUCCCCUAAUAUGAAAAUAAUAAUACAAGAAAAGGAAAGG
GGGUGUUAUGGCCCAUUACAACCCAUGAAUAACAUAGACAAACAAAUAAAGAGUAAGGGA
UUUUGGGACCUAGAAUGCUACUGCUUCUCUUUAAUGGGUUUCAGCCCAUUUUAUUUUGCU
GGAUUGUUACUGCUGCCGAUGUUCAUGGGCUUGGGCCCAUUUCCAUUUUGCUAUUUCGUC
GUCUUCAGUCCAUGAAGAACUUGACAUGGGUUUUAAUUCAAAAUGCAAGAGAGAUAAGUC
CAUGAUCAGACUCGAAUAUAGGAUGUUCAUGCAGAGAAAAGGAAUAAAAUUAGACAUCAA
CUUAAACAAGAUAAAUGAAUAAAAUCAGAGUUCCAGAAGUCCACAGACAAGAAGAUCUAA
AUCAGGCAAGUUUAGGUAGAGCUGGAUAAAGUAGCCACUUCAAACAUGCUUAAAGAAGAC
UGAGCAUGAGAAUAGGAUACAAGAUUUAUGUAGUAAAACACAUACAUCAGAAUCAUAGCA
ACCUAAACUUAACAAUGUUUAUCUCCUUUUGUUUUAGCUCAUUAAAGCAUUUAUGGGAAA
AAUAUUCUCUAGUCAGACCAACUAGCACACUAAAAUAUACCUGAUUGGGUUAUAUUAAAA
GACGACAAGAAGAGUAGGUUUUCCAGUCCACUCAAUAACCCAUGGGCAAUUAAAAUCAUU
AAUCUUAGCUUGACAAGCAGCUGAAACAUGUUACUAGGUGUUCGAUGAAGAUCCAUCUUU
UCUUAAGCUCCAUGGCUAGGAAAGCAACUAAGACUUAAGACCAACUCGAAAACAAAUAGG
UAGAGACAUGCCAUGAAGAACUUGUUCUUACUAAUAAACUACACGCAACUAGAGGGAUUA
AAGCUAAUAGAAUGUAAAGCAUAUAUGAACCAACCGAUUUCAUUCAAGCAGACUUAAAUA
UGCUAAGUCUUUAAUAACAUGCAGGCAGUUGGCCCUAAUCCAAAUGGUUGAAGACAUAGU
AGGGAAAGUGAUAAUUUCACCUGUUUACUAAUAAUGGAGCAUGGAUCCAAUGACUUGUAU
CUGAUAAAGACCCAUUUUUUAUCAUGAGCUAGGGACUAGGUAACUUAAAACAUGCAACAA
GCAACAAUUAACAAGGAACCAGUCUAACAUCUAGCAAGUGAAUUGCAAAGACAUAUUUAA
AGACCCUUUGGACCAAAACAAAAACAUAAGUCAUGGUUCAGAUAGGAUAAUAAGACCCAA
UCCAAACAAACCAUUAAAACUCAUAAUUUUGUUUUCUUUUACGUUAUACUUAUUUAUGCC
UCUAAGCCCCACACCAUAGACAGCACGCAUCAAUACUCACAUGACCGUUUUGUGUCAAAU
AUGUCUAUCUGAAUGUUCAAACAGAGGUUAUAGUUAAUAACCUAUCAAAGCAAGUGAGAA
AUCAUUCAAAGACAAGGGCUUUAUGCAAUUCCCCCUUGAAACAAAAGUAUACAGGCAAUG
CCUCUAUCAACAGACAUAAGAAAAUAUGACAAACACACUGUCUUAUUAGAUUUCAACUAA
AGACUCUAAAGUUUACGCAUAAAAGCAUGAUCUCUUCCAAGAGAAGUACAAAAAAAGGGA
CUUUUAGGAGGGUAAGCAUGGUAAUGAAGAACCUUGCCUCCUCUCCUAGUCCCAAACUGU
UUGUGGAAUAUAUGUAAAUCCCCAGAUAUGCUGACCCCAUACUUCAAUAUGGCACACAUC
CAACAUGGAUAUCAACAUAUGAGAUCAUAUAAGGAAUCAAACUUUAUCACCAAACCAACA
CAUUGCAACUGGAGAGAUGGAUCUUAAGAAGCACACAGACCUAUAAGUCUAUGCAACAAU
AUUCAACAUGCUGAAAUUUUGAAGAAAAAUCCCUUCGUACUAAACAUUAUUAACUCAAAG
UUAGGAAGAACUUUAAGAUACCCUCACAAUGAUCCCCUUCAGUAGCAGUUAAACAAGUAG
GUUUCUGGAACACAUUAAACAGAUUCCAAUCAUAGUUUAUUAUCUAGUGCUUAAUGCUAU
CAAGUCUAUCAUUU

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 [-536.04] kcal/mol.

2. The frequency of mfe structure in ensemble 1.24723e-25.

3. The ensemble diversity 359.87.

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