lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-309.10) is given below.

1. Sequence-
ACAAACGCAUAUCUUCACCCAAGACAAUCUGCAUCUGUCAAUCUUGUGGAAAUCAGCUAA
CUUUUACAUCAGUUCAGCAUUCCAAGCGAAAUGACAUUUUAACUCCAUGUUAAAAAAGCU
GGGCUCAUGCUGCAAUAACAGCAAAAAUAAGCAGUUGAACUUGAACUACAGCCAUUACCA
AGCAUCUGUCAACUCUCCAUAGAUUCAAAAUAAUAAAUCAAACAGCAAUCACCACCAAAA
UUUUGGAGUCCAAAGUCAGCAGUUUUAUCUAGCUGAGGCAACAUGCGAUUUAAUGGAGGA
UAUGACAAGGGAUCAUGAGAUUAGAUUUUUCUGGCAAACAUAACAAAAACUUUCGGCAUA
GUUGCCUGUUACUGUCGGAAAAAAAAAAAAAGAACAAGACUUGAUCAGCAACCAUACAAC
AACAAAGCCAGUACUUCAGCUACCGUAGUAGUCCCGAAAACGCAUAUAUAAACUUAUUGU
CACAUAAAAGCACUGAAGAAACAAGUUGUGUGUGUUGUUGAUGAAAGCAACCAGUAACAC
CUCUCAAUCAAUGACAGAUGGAAAAUAUCAGGACCAAAAUUACUCAUGUACAAGACUGUU
AGUCUAACACAAAAAAUUGCUAAAAUCCCAGAACAUGCUCUCACAUUACCAUAUUUUUAC
UCUUAGUAUGGCUUGACGCAGUUAAUAAUAGUGGAGUCGAAAAUAAGUAAUAUAAUGUGA
AAAAGAUUACAUUAAAAUAGACCUAAAAGUUAGUCUUUCGAAGGUUAUUGAGAUUAUUUA
GAGAUGGCAUGCGACACUUAAUAGUGAUAUAUAACAAAGUAACUGGCAUAUAAAAUAAAU
CAUGGAAUAAGAACCUUAGGAAGUUAACAAUUUAAUGCACACAAAAGGGAAAUCGUAUGA
UUUCAUUGAGAUAGAGGGAGUAAAGUAGUGUUCAAUAUACAUCUUAAGCAAGUGAUUUCU
UUUUAGGAUGAACUAAGGUGUUCCAUUAAUAUAUUUUAAAACUGAUAAGAUGUUCCAUUA
GGCAUCCAAAAGUCACAAAAGUAGUAGAUUUUCUUCCCAAUUGUCUAACCUUUGGUCAAU
AGAGUUAUCCAGUAUCUAUACUAGUUGGACCUAAGAGUAGUGAAGGUUCGCAAGGGGCAA
GCUGACCCAGACACCACUAUUAUCGAAAGAUGUGCACUUAGAAGUAUCAUGAAAUCAGAA
AGACAAACAUAUAUUAUGUUUAAACAUAUAUUAUGUUUAUUACCAUAAUGUAGUUUAGAU
CUGUCAUGUAUCCAUUUUUCUUGACUUGAAAAGGAUUUUACAUUAAAAUGCCAUCAUCAU
CAUCAUCAUCAUCAUAAUAAUGACACUUCUUUUCUAGAAAGAAAUCAAGACAGAUAAAAA
UGCAGAAACCAGAGUGCUUCCGUCUAGCCAAAUUACAUAACAGAUAAAUGAUAAGAAUCU
UGAUGUCUUUCACCAGUUUCAGCCCAUCCAACAAAACAUACACAGGUUCUGUUGCCAAAU
GUAUUUGACUUGAAAAGAUACUCUUAACUAAACAUAAUAUAAAGGAUAACAAAAAGAAAG
CUUUCAAAAGGUUCAAACAUCAAAUUUGAAACUACAACCAAAAAAAAAUAGUAUGUAUUC
AG

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 [-336.15] kcal/mol.

2. The frequency of mfe structure in ensemble 8.62265e-20.

3. The ensemble diversity 462.55.

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