lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-584.30) is given below.

1. Sequence-
UGUGUAAUUUUUAAAGUGGACCCCAGAGUUCCUUGACCACUUCAUCAAAGCUUAAUUCGU
UGUUUGGUGCCUUGCUGAAGUGUUUGGGGGAACUCUGGGGUCCAUUUAAAAAUUACACAA
ACAAGUAUAAGUGCAAGACUAUUAGCUGGAGUCUGAAGAUGAUGAAUGCAAUGGUUUAUG
UAUAAAUCUAUCAAGGUGUUCUCUAGAGUUCUCUUAACCACUUUAUAAGGGCUUACUUUG
AUGUUUGAAGCCCUGUUGAAGUAUUUGGGGGAUCUCCCUGAUUUCACUUUGAAAAUAUAA
GUGCAAGAGUACUAGUUGCAGUCUGGAGAUGAUGAAGGCAAUGGUUCAUGUACACAUAUU
UUAGGUGUUCCCUAAAGUUCCUUUGACCAUUUUGAUAGGGCUUACUCCGUUGUUUGGAGG
CCUACUGAAGUGUUUAGGGGAGGUUCUAAGGACACUUUGAAAAUUACAAAAACAAGCUAG
GUUUAAGUACAAGACUACAAGCUGGUCUUUGGAUGAUGAAUGCAAUAAUUCAUGUAUAAA
UUUAUCAAGGUGUUCCCUAGAGUUUUCUUAACCACUUCAUUAGGGCUUAUUUCAUUGUUU
GAUGCCCUACUGAAGUGUUUGAGGCACUCCGUGGUUCAUUUCUUAAAAUUACUGUGUUGG
AGUCUAGAGAUGAUGAAUGAAAUGCUGGUUCAUGUAUAAAUCUAUCAAGGUAUUCUUUAG
AGUUCCCUUGACCACUUUCUAUGGGAUUACUGUGUUGUUUGAAGCCCUGCUGAAGUGUUU
GGGAAACUCCCUAUUCAUUUUGAAAAUAUAAGCGCAUCAGUACUAAUUGAUGUCUGCAGA
UGUUGGACACAAUGGUUCAUGUACAUAUCUUUAAGGUGUUCCUUAGAAUUUUUUUAACCG
CUUUGUCAGGUCUUACUUCGUCAUUUGAAGAGCCGCUGAAGUGUUUAAGGGAACUCCUAG
GUCACUUGAAAAUAUAAUAUGAUCAUCUUUUUCCUGGGAAUGUCCAUAAAAUAAAUGUUA
CUAAUCCAAUGCAUCAUCCAAAAAGACACAUCACGCCUCCCUUGUUUAGUUUUGUUCUCU
GUAAAUCGCUGCCUACUCAAGCUUAGGCACCAUUUUGAUUCACCCUCUUUAAAAACAAAA
CUCAUAAUCACAAUUCUUCAUCAAACUUUAUCUAGUCAGGAAACCUUAAGGCUUGAUUUA
GUUCUCGAGGCACCUUCAGACAUGUAUACUUUUAAAGCACAUUUUAUAGUUUGAAGUCUU
CUUGAAGUGUUUGGGGGAACUCCAAGGUUUACUUUGAAAAUUACACAAACAAGUAUAAGU
GCAAGAGUACUAGCUGGAGCCCAGAGAUAAUGAAUGCAAUGGUUCAUAUAAAUCUAUCAA
GCUGUCCAGUAGAGUUCCCUUUGACCACUUCAUUAGGGCUUACUUCUUUGUUGAUGCCUU
GUUGAAGUGUUCGUGAAACUUUGAGGUUGACUUUGAUAAUUACACAAUUAAAUAUAAGUG
CAAGAGUACUUAGCUAUGGAGUAGGGAGAUGAUGAGCACAAUGGAUGAUAUACAAAUCUA
UCGAAGUACUCCCUAGAGUUUCCUUGAAUACUUCAUGAGAGUUUAAUUUAUUAUUUGAAG
CCAUGUAGAAGUGUUUGGGGGAAUUCCUGGGUUCAUUUUUAAAUUAAGCAAAUAAGUGUA
UGUCCAAGAGUACUAGUUGAAUACCAGAGAUGAACGCAAUUGUUCAAGUAUAAAUCUUUG
AAAGUGUUUCCUAGAGUUCCUUUUGACCACUUCCUGAGAACUUACUUUGUUGUUUGAAGU
CCAGCUGAAGAGUUUGGAGGAACUCCCAAGGUUCACUUUGAAAAUUACACAAGUAUAAAU
GCAAGAGUACUACUUUUAGCUCGGAGAUCGAUGAAUGAAAUGGUUCAUGUAUAAUUAUAU
UAAGGUGUUUCCUGGAUUUAUUUUUACCAUUUCAUGAGGGCUUAUUCUAAUUUUGAAUCC
AAUUGAAAUCUUUAGAGGAAUUCCCAACUUAUCUUUGAAAAAGAUUAAAUUUUAUAUAUG
UACUCUGAUAGCACUAUUACUUCCAAAACAG

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 [-620.85] kcal/mol.

2. The frequency of mfe structure in ensemble 1.74412e-26.

3. The ensemble diversity 563.66.

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