lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-359.80) is given below.

1. Sequence-
AAAAGAUAUGCUAAAAUGAUGCAAUCACAAUCAUGGGUCCUGAAAGCAUUAUAAUAUAGA
ACAUAAUUGUAGUUAACCCUACUGAGUCUCUCGCAAGAGAAGCAACCCUGAUUUUCUAUU
CUUGUGGUUGCUUAAAUAUUCACUCAAGCAUAACUAUGUCAUUAGCUACACAUUAGAAUC
ACAAAAUAUUGACAUUGCAUACUUUAAACCACAGAAACUCCAAUCAUGACUUGUAAAAAC
UUUGUUAGUUGAAUUCACUUGAAAUCUCCAACGGCUUAGCUGCACCAGUACGACUGGAUA
AGAGAAACAAUAAUAUAUGGUUAGAUGCCAUAGCAGAUAUUAAGGUCUCUUUUGCAGCAU
AGCAACACUUGGAAAAAGGAUUAAAGCACCAUCAACACGAACAACCAUUUAAGUACAAAG
AUUGUUAUUAUCCAUGAUUCAAAAUAUAGCACAUAAUCCAAAUGCCCAAGAAAUCAUCCU
CCAGGAUUGUCUUGGUCGUCGAAACUAAAAUGGAGAGGCUUCGCAGAUCACUCAGUUAUU
UCCUAAUAUAACAAAGGUCUAUGAUGAAUUUAUUGGUCCUUGCCUUAAUGCAGCAAGGCU
CAGCCUUCCACAUGAAUAAGACGAUGCAAUAAAAGGAUAAGCUUACCUCUACAUACUCGG
CCAAAAGUGUUACGAACUAGGCUAACAUAGUUAAUAAUAAGGUAUUCAUCAAUUGCGACU
CACACAAUAAUGCUGUACUACUGCAUUUCUACUGAAGAAACAUAUCUGAUUAGCUUGAUG
CAGUUAUCAAGGAAUAAAAUACAUAUAUUUUCCCUGCAAACUAUGGUACCAAUUAAGCUU
AGAACUAUUUUAAAUAAAGACCAAUCUUUAAGACAGACAUCAGUAAAAACUCAGGUAUUA
GACAAUCAACAUAGGAACAGUUUGAUUUUCCAAUAGAUUCACUCAAAUUAAACGGAAAAU
UCAAGUUCCUGGCAGUUAUCUGAAUGCCCAACUAUCUCCAUCCAUAAUCUAAUAAACACA
GCAAAGAGCAUCUCAAAGUACAGAUAUCCAGCCAUGAAUGCUUGUUAAAAUUGAACAAAA
GAGGUGCCUUUACAACAACAACAUACCCAAUGUAGUCCCACAAAGUGGGAUCUGAGAAGG
CUAAAGUGUACACACACCUUACCGUACCUCAGAGGUAGAGAGUUUAUCGGAAAUAGACCC
UCAGCACAAGGAAAAGAGGUCCUUUACAACGACAACCAGUACAGUCUCAGAAACUGGGGU
CUCGGAAGCAUAUACUGUAUGGGACCUUACCAGUUACCCCUACCUGAGAGCCCUACCUGA
GAGUAGAGAGCAUGUUUCCAAUAGACCCUCAGCUCAAGGAAAAGAGAUACCUUUAGUCAA
ACAAAAAUUCACAGACAACUGAUAUAGCUCAAGGAAAAGAGAUACCUUUAGUCAAACCAA
AAAUCACAGACAACUGAUAUAAAAUAAUGCAGCAGCAUACUAGAACCCUCACCUAAUUAC
AAAUUCCCCCCUUUCCCUCUAUCCAAUUAACACAUUACAACAACAAUAACAACAUGCCCA
GUGAAAUCCCACUUGUGGGGAAUGAAUAGGGUAGUGUGUAGGCAGCCCUUACCGCUACUU
GGUGGAGCUACCCUUGAGUACAGAAAAUCAAAGUAGACAUAAAAAAUGAAAAUGACAUCA
AGAAAACAUAGCUACAAAUAAGAAACAGUAACAACGAAAAAAAAAAACCGAUAUCCAAAA
CACAGUAAACAACAGAUUAUGGUAAAUCCAAUCAACACAUUGCAACUAAGAAAUUUAAUC
CCAUGAAGAUUACCAGAUGUAUAACCAAAAAUUCGAGAGAUCACCCCCUUAACAAAACCA
AGAAAGGAAAACAAGGAAUACCCAGAUAAGAAAAACUAAAAUCCUCAUUAAAACAACACC
AA

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 [-397.27] kcal/mol.

2. The frequency of mfe structure in ensemble 3.92931e-27.

3. The ensemble diversity 419.75.

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