lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-338.30) is given below.

1. Sequence-
CCCUGCAUGACAUAAAAGAAUAACUAAAAAUAAUGUCAAUUAUUUAAGUCGCCCCUCCAG
UUCAAGUAAAUUAAUUAGACCUUCAUUUUAGUUUAAACAAUAUUAUACUCUCGAAAGUUA
GACGUAUCCACAUAUAUUCUAAAGCUCCAUUUAAAUGGUUGAUGUCAUAAUAUGCUAUUA
UGCUUAACUGUAAUCCAGUCAAUACCCUCCAAAAGACACUCUUCCUCUUCCCUGUUGAGC
UUUGAUCCCCUCACUCACACAAACUCUAUUUCCCUUGUGAACUCGCAUUAGUCACCACCA
UCCUUGAGACCUUAACCUUUGUCAGAUAUCCUCCAUGAGUCCUCAGUACCUAUCAUGGUA
CUAUAGUUUCUUUGUUUAUCUUUUCUUUUUAUCAGUGUCGUUACCUUGUUUAUCUCAUUC
UGAAACCCCUUAAGGGUCUUCUUUUUCCUUUUCUUUUUCUUUUGUCCAUCUUAUAUAAUU
AUUUAUGAUUGAACGAAAAUGAGGGAUUGGAUCUACUUGUUUAUGCUUUUUGGUAGAAGU
AAAAGAAUGUCGAUUCUACUUGACGAUUGAUGAGGAGAUAAGACUUUGGACUUGACUCAA
CCCUAGAAGCUAACUAGUGAUGUGAAGACUGCCCAAGACCAUAUAGGAGCAACACAUUUC
CUCGGACACUUUGGAAAUUCUAAUCCUCUAUACCCCUCUCCUCGCUAGACAUCUGGAAUG
UGAACAAUAUAAUGUGACGGGCCCAUACUAGGUUGGUUUGAUAAUGUUAAGAAGGUAGAC
ACUAGGUCUAAAAUUGAACCACCAAAGGAAGCUCAUAAAGUAAACAUUGCCCAAGAUGCU
AUAAGUAGAAUCAUUCUUUCAACCAAUGUGGAACACGCUAAUAGGGGUUAAGGAAGAAAA
AUAUGGGAGAAAAGCUUCUCAAGGAUUUGGAGAUGGGUGAAGGAAGUAGUUGGAGUAGGA
AGCAGAAGAAGAUUUAUUACACAGAAAACAUAGUGCAGUUAUAUCAUGAAUGUCGCUGAU
CUAUUCCAUAUGCAUCAAGUAUGUUUAGCACCCGAAUAUCUGCAGACAACCUUUGACCUU
UUUAACGGUCUCAUUCUGUGGCUAGUCCAGGAGUUCCAGAUCUUAGUUUUCUUUGAAGCU
GCCGUCAGAAGCUCUGUCCUAGCCAUUUUAAUAAAAUUGUUUGAGGCUUUCUAGUUUUUG
UUUACUGUUAUUCUUUUAGGCCCAGGAAGGGUUUCAAGUAUUAUUUUUUUUCUUGGAUGA
UGCUGCCGGUGGUGUAUCACAGGAAAAGAUAGCCCUCCAAGGAUCUUGGGCACCCUAUUC
AUAGCAGAAGGAACAACAAUCCUAAGAGCUAAAAUGACUACAUCAAAAGCUAUUUGGUAU
AUUUUCUUUCAUGUGCUGGCAAGAGAACUAUGGCAAUACUACAAUUAAAAAAACUCCAAG
UAAAUGACAUUUUAAUAUGGAUAUAAAAUUUAAUCGAGGAUGUCAAAUUAUUGCCAUUCU
ACUUUGAUUAGUAGGAG

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 [-367.64] kcal/mol.

2. The frequency of mfe structure in ensemble 2.09948e-21.

3. The ensemble diversity 333.36.

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