lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-435.75) is given below.

1. Sequence-
AAAGUGUUGUCAAAAAAGAAAAAAGGAUAUUUUUUUUGGAAUGGACUAAAAAGAAAAAAA
CGACAAACAAUUUGAAACAAAGGGAGUAUAAUUUACCAACCAAAAGAAAAAUCUUUAAGG
GACUGAGAAUAUAAGAAAAUUAGACUACUGUUAACAAAAAAUAUUUACUUAGGUGGUGAG
AUCAAGAAUUUCCUCUAUGACACCCAGAAUUUGUGUAGACCAAAAAAACUAGUUAUACAA
GUAGCUCAACUAAGUUUCACAAAUGAGAGGUGAGAACCUCCCACCUCCCUCUCUUUUUAA
GCCACAACUAAGGGUCUUACUACAAAAAUAAAAUGAUUCUAUACUAUAAACAUGAAUUCC
GCACGUCAGAAAAUUCCUUAACACAAAAUGCAAUAACUAGCCUAAGAGUGAGGUAGAGUG
AUGAACUGAGGAGCAUUUUUUUACAAAAUCAAAGAUUUAGAUUCUUUAGUAGCUUCAGCA
GGUCUCCCGUACUCUCAAUUCCCCAAACAACAAUUAUCCAUUCACCAAAAUCAAUCAACU
AGGCUCAAUCCCAAAUAGUUAAUGAUCUGCUAUAUCAAUCUUCUAAGUCCAUUCCGCUGU
UCUCAGAUCAAAAUACAAUCCUAUUCGUUCCACUCUUCUCAGAUCAAUCUAAUUACAGUC
CAAUUCAUUCAAAAUAUUAAUUGCCGUAAGUCCAUUACAGAUUGAACAAAUCUACCUACU
AGUCCAAACCUCUUAAACAUAGCAUCAAAUUAAACCUAAUCAUAAAUCAUAACCAAGUAA
CCACUCAAAAAUCCCAAAAAUCAACAUUUGUCGUCCUUUAAUGUUAGGUCAUUACAAUCC
UCUGCAGAAAACUCACAAUCUGCAACAUCAACCAAGGUAAAUUCCAUUUCCCAUGAUUUU
CAGCAGGUCUCCAGUUAUCAAAACUAAAAAAUAUUCAUUCAACACAUUUCACCAAAUUCU
UAGCCCAGUCAGCUUUAACGGCUCUUUCCACCUAUGUUGCUCGGACUCUUCAAAAAUGUC
UACGCGUCUACGCAUGCUAAAAAAACUGUCCAAAAUUUAACUAAAGGUCACUCUUUUCCU
AAAUUCUAACCUUACAAAAGUUAGAUAUACCUACGCAGAAUUAUCUUUAUCAGAUAAUUC
CAAAUUCUCAACAGGAUUAUACCCGUAAAAUUCACAGACCCAGCAACCUCAACCACAGGU
CAUCAAGAUAAAUGCACAAAAUCCUCCAUUUCCUGUGAUUUAAUGCUAAGUAUCAACUGU
ACAGCUUAGUUGCAGUUUCAGCAGGUCUCCAGUUAUCACAACCAACAAUUAUGCAUUCAA
CACAUCUUACCAACUUCUCAACCCAUCUCAGCUUUAAUAAUUCUUCCCACCUAUGUUGCU
CGGACUCUUCAAAAGUAUAGGAUACUCCAAAAAAAUUAUUUUUAGAGAGUCCGAGCAGCA
UAGCUUCCCACUAGUCAAAAAACUGUCCAAAAUUUAGCUAUCUGUAUCCUAAAUUCUAAU
CAAAGUUAGAUAUAUCAUAUACCUAGGCACAAUCAUCCUUACCACAUAGUUCCAAGUUCU
CAACAGGAAAAUCUUACACAUCACACUCACCAAGCCCAACCACAGGACAAUAUACAAAUC
CACAAAAGCCUCCAUUUCAAGAUCCUCAAUUGAAAUAUCAAAUAGGGUAAUUCUUAGCCC
AUCUAAGCUUUAACAAUUCUUUCCACGUAUGUUGCUUAGACACCUCAAAAAUACUGUAUA
CUCCCAAAAAAAAUGUGGCAAUGUUUUUAAAAAGUCUGAGCACAUAGAAGCCACCAGUCA
AAAACCUGUCCAAAAUUUACUUGAGGUUUGCUACUCAAAACGAGAACAACAUUUUUGGAG
AGUCGGAGCAACCUAGCUUCCCACUAUAAAAAACCUGCCCAAAAUUUACUGAAGUGUCUG
AUACUCAAAUAGGGACAAUAUUUUUGGAGAGUCCAAGCAACCUAGGGUUCCACUAGUUAA
AAGAACUGUCCAAAAUUUACAAAGAGUCCGAGCAACAUAGAUUCCCACACAAAAAACUUU
CCAUAAAAUUCAACCAAAGUUCCCUCCAACCCUAAAUUCUAAGCAACGUUAAAGAAAUAU
GUAAGCACCCGUAAACAUUUAGCAAUCCCGACGAGAGGGCAUUAAUAGAAAUUCUACAAA
AUCCUCCAUUUCAACGUCCUCAAUUGAACCAUCAACUCAGAUAAAAACGAAACAAAUUAG
ACCCGUCAUUGUCAGUUAGGAAUGAGGCAAGGCAGAGAGCAAAAGACGGAAAAUCUAAGU
GCUCUACAAACCUUAAUCGAUUGGAUCAAGGCAUAAUAAGUAGCUGUAUUUGGAGAAUAA
CCAGGUGAUGGGUACGGAUAGCACCGAGACAUCCUCAAAAAUGAAUUAUUCGAGCGAAGA
AGAAAGGAAAUCCCACAAGGCACCGGAUAAGCCCCCCAAGUAUCGGCAUAUCAUCUCAAU
GGAGUUGUGGCCUG

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 [-479.88] kcal/mol.

2. The frequency of mfe structure in ensemble 8.06278e-32.

3. The ensemble diversity 603.85.

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