lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-469.70) is given below.

1. Sequence-
CGAUAGUUUAUCAAUUAAAAUUAAACAUCGACCUAGGAUGUUGUCUAUCAAGAAAGUGGC
ACAUAUUUUCACUGCCACCAUGAUCCCAAAAUUUAUUAUUACAACUUAAAAUAUUUGUAU
AAAGUUAAAAUACAUAAUAAAUAAAAACAUGAAACAAAACAAAGAUUUCCCCCUAUAUCA
AUCCCAGCAACUCUUCUCAACACUCUGGCCAAACCUCAUGGUAAAACCUAUAAAGCAAGC
AAAACUCUAUCCUGGUUUAAGUUUGGAGGGUCCCAAACAAGCCAUACGGUCCUUCAUCGA
CAUAAUAAGAUCAAGAGAUUCUCAUUGAGUCCAAGCCUAUUGUGCUAAGAAGUAUGGAGU
UUGUGGGAUCCCCUUUACUUAAAUCGGAGUUCCACAUAAAAUAAGCAAUAAUACCUAAGA
AACAAACAUGCAAUGAAUUUCCUAUGGGCAAGAUUUCUAAAGCACGUUGAAAAUAAUACU
ACAAAUAUUGAUUGCAAUAACGUAGCAGUAUACCUCCAUAAAUACAUGUAAUAUCAAAAA
GUAGUAAUUGAAAGAAACAAGAAAACACAGACAUGCUUUGGAAAACAAAACACUAGGAAA
CUAUUACAUAGAAAAUUUAAAUGCUUCGACCAAAACUAAUCGAUUGAGGUACAGACAUAU
AGGAAAACAAGAAACAACAGGGAAGCAGUAGUAAAGUGAGCCAAAAUCAGAAAACCAAAG
CAAAGUAGAACUAGAGCAGGAUAUCUUUUUUUAAAUUUUUUUUUAAAAAAAAAACUUAAG
AGUGAAAGUUAAGAAUAGAAGUUGAAUAUUACAUAAGAGGUUUUAAGUAUGAGGGAAGAU
AUGAGUGUUAAAAAGUGUGUUUGAAAAAAAUGAAAGGGGCUGCAUAUAUAGUAGCAUAAG
AGGCUAGCUAAUAUAAAGGAAGAGAAUAAUUUAAAAAUCAAUUAAGACAAGGUUUGCCUA
AAAUGGAUGGCGUAGAAAUAAUCAAAGGCUAAAAUUAACAAAGUUUGCUUUAAAUUAUUU
AAGUAAGAAUCUGUACAAAAAAAUUAUUGCAAGAAAAAUCAAUCACCACCCCUAGAAAAC
CAGUCAUAAUAAUCUGUCUCCUGUAAUUCCGAAAAUUGAAAUCAAUUAGAAGCCUAAAGA
GAUAUUCAUCCUAACAUAGUUAGUCAAGUAUAAUCGCUCUAGACUAAAUAAAAGGAAAUA
UAGUAAGAGCACCAGAAUAGAGGAACAAAUCAAAUUUACCACAAAGUCAGCUGAAAUCAA
GGCUAUCACAUAUUAGUUAAUGAAAUCAAAUCGUUUAGACACUCAAAAUUAGACCAAGUC
UAUUAUUCAAUUGAGGAACAUAUUAUCCAUCAAGUUUGAAUCAAUCAAAGUCUACCAAGU
CCAUAAAAUACCACAAAGCCUAUUACCAAAUUUAACACAAUACAGAAAAUAAUUUUCGAG
GACUUACUGAGCAUGAAUUUAGAUAAAUAAUUAGAAAUAACAGCAAUAAAUUGGUGACCA
CUUUGUAAAUAGGAUUCAUAUAUGAGUAAAGAAAAAUCUAGCACAAAAAUUGAUGAUUUU
AAUGCAACCUAAACAAGUUGAUAAACAUAACCCAAUAAACAAUUAGUCAAGGACUUCAAC
AAGAUUUUGCCCAUUUUAGAUUGGAAAAAAGAGAAAAAUAGAAGAAUAAAACAAAAAUAA
UGAUCUGGACAUAGAAAAAACAACAAGAAACAAACUCGAAAUGAUAAAAUUCCUCAUAAA
AUUAAAUUUGUUUUGGUAAGGUUUGGCCGAAGUAGUGGGCUGAAUCUAGUGGAGCUUCUU
GUCAUAGAGUUGCUGAAUCUGAUGGUCAAGGUAGCAGCACGACGAUAUUGCUUAAUAAAA
AAGGAUCUUCAUCAUGGUGAACUCAUCGGAUCAAUAUAGGUGAUUUCUAAUGGAUUUCCA
AUUCGUUAUGGCAUAGAGUCGACAGAUCUGGUGGUAGAGGGUUAGAUCUGUUUGUGGCGG
CUUGAUCAGAGGUCCUGGUGGACAUGAUCAGCCGAUGGUGUCCAAAUCUAGGGUUGCUUG
UGGUAGGGAUAUGUGGGCGAUGUCGGCAUAACAACUUUCUUAAGCCGCGAAGUAGUGGCA
GCAUGGUGUAGAGAAGAUGAGAAAAGGGUGGUCAUUUGUUUGUGAUAGAGUAGAUGGGUU
AAGAGAGAGGGGUGAACGUACUAGAGAAAGUAUGAAGGGAGAGGGAGGGCAGGCCGGCAU
UGUGGUGGUGACUGGAUAGAACUUGGAGAGACGAAGAAAGAGUUAGAGAAGAGGAAGAGG
UGGCUAGGGGAAGGUGAGAAUGUGUCAAAACCCAAUUUCUUAGGUUAUGUGGG

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 [-511.42] kcal/mol.

2. The frequency of mfe structure in ensemble 3.97672e-30.

3. The ensemble diversity 462.00.

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