lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-399.80) is given below.

1. Sequence-
GUUAUGAACUUGAUCGAAUAGGGUUGUCACAUAAAUAGUAGGUUAGUCAAAGUCUAGCAG
AAGAGUUCUCCUCUACAUUGUGAUUGUCUUUUCUCUACAAUUAUAAAUAGAAAUCCUCUA
CAAGGACAAAGAAAACAUCAAAAGCUCAAGAAAAGCCAGCAAAAACUCUCAAGAACAAAC
CAUUUUUUGUCUUCCUCUGAAUCCCGGAGUCCCAAGUCCAACAAAGAAGUUCAAAUCAAU
AUUUCAGAACGCCACUAGUUCUGCUGCAGAAUCAAGUGAUUGGGACUCAAAAUAGGUGAC
CAAUACCAAACACAGCCUUCUUUAAUCCUCCAUUCACCACUGUACAUCGAUGGUGAUAAU
UUCAAUUCAUGUUGACUGCUUGCAUCAGGAACUUCAUGAGCCGCUCCAACUGUGCAAUUA
GUCACAAAAUUUUCUGGUACCAUGCAGAGUACUUUCAAUCUGAGAGAAGAAAUGAAAGUA
GUAGGUUGAAUGUGUUUCAUUAAGCAAAUAUCUAACCAAAUAACUAGCUGCAGCAUGAAG
UUUUGGCGUAUACAAGAGUAAUGAGCAAACACUACCUUGUAGUGACUGGAUUCAAACUUU
CAUACCUUUUAAACGCCAUUUAGUUCAGUAGAAAGAAAAUCAGAAAAGAUGAAGAAUUGG
AAGAUUUCACUCAAAUAGGUAAGGAGUUUUUGGCCAAAAGCAUCCCUGAAGUACACUCAU
AACUUCAAAUACAUCCUUAAAUAUUUCUAUAAGCAAAACAACAUCCCUUAAAGUAUACUC
AUAUCUUAUCACUGUAAGCAAAAAACACCCUUCAAGUUCAUUGAAAUGAGCAGGUUACAU
CCUUCUGUUAUUAAUGGUUACAAAAUUAACAAAAUCCUCAAAAUCAUGUGCAAGACAUGU
CAUCUUCGCCAAAAACACCAUGGUUCCCUCAAAGAUUUUUGAAGUCGGUACAUAACUUGA
ACCACUUAAAUCGUGCUUUAAACAUGAUUGGAGGAGAUUUCAAGGGAUAUAUCCCUUUCC
UAUUGUUGUAUAAUUUGUUGUGAAGAAGCCAGCCAAUUCAUCCUUUUCAUCACUAGUAAC
AUGAACAGUCAACAACAUGCAACAGAAUUGCAGAGCAUAGUAAGAAAAAGAUUCCCAUCU
CUUCCUCUGUCUCACCAUCAAGUCAUUAAAGAAAAAAAGAAUAAAACCCACUUCCUCCAU
UCACCAUUAUCCUUCACAAGAAAAAGAUUCACAGUAUAUAUUUGUAAGUUCUGUAACAAG
CUUUCACUACAUUAGAUCCUAAAAAGUGAACUAAUAAUCCAAACGUAGAUGCAGCAUCCA
AGAGUGUGGGCCUAGUGGUCAAUGAAGUGGGUUGAGCACCAUGAUGUCUCAGGUUCAACU
CCCAGUAGAGAGAAAACACUAAGUGAUUUCUUACCAUUUAUUCUAGCUUUAGCGGACAAA
GUUAUCUGGUAUCUAUUGGUGGAACGUAUCCCGUCGAAUUGGUCAAGAUGUAUGCAAGCU
GGCCUCGACACCACAAAUAUCAAAAGAAAAAAAAAAAGAACAAGAAAUAUAGGAACUCCA
GAAAAGCAGAAAUAGAGCAGCCCGGUAUACUAAGCAUCCUACUUUCACGCAGAUUGUAUG
AACUUCUUCUCAUUCACUGUCAUUCCCACUCUUUGCUCCAUUAGGUUCGAUUUUCAACAA
AUGAAAAAACACCACAGUCGAGACUAUUAUUCCAAUUUAGGAGUGCAUGAGGAACACGUA
ACCCUAUUGCAGGAAGAAAAUCUCUGUCUCAAGUCUUUUCCCUAUAAUGUUUGGAUUUUG
AAGGAGAAUAGAGGUGGUAUUAGUUUAACAGAUUGGUGAAUUGAAAUAUCUAAAUAUGUA
UUCUAAAAAUUAGAGGACUUUAUUAUCAGUUGAAGUCAAUUCAAAACGUUUAUCUAACGA
UAACACUAGCUAACAUUCCUUCACUCCAAAAAGAGAAAAAAAAAACUAACUACAC

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 [-436.89] kcal/mol.

2. The frequency of mfe structure in ensemble 7.29657e-27.

3. The ensemble diversity 469.61.

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