lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-585.70) is given below.

1. Sequence-
GUAGAAUAUGUUCCAUCACCAUUAAUUAAACUUAAAAAGUGUCAAGUUGACAGUCUGUUA
UGUUAUCCUAUUAUACUUGUUUAAGGGAGGGAGUUUUUUAAAUGUUUUUACGAUUUAAUC
UUCAGUCUAUCUGCACCUAUAACGUAUUCUGUAGAUUAUACCUCAUUUCCCACUCACCUG
GUUCCUUCCCUGGCCUCUUGAAAACCCCUCUCUAACAAAAUAUCACUUUGUAUUCUUUUU
GUUAGUAAUUUUUUAAUGUUAACUUAAAGUGGACAAAAAUACCUAAUCCAUUACUCUGAU
GGUUGUAGAUAAGGUCAGGUAAGUAAAUGUUCAUUAUGAACUCUUGAGCGAGUAUUUUGU
CCACCUAGAGAGUAGAAUCUCUCUUGAGUAAUGCUAUUGGGAUCAUUUAUGCUGACUUUU
UUGAUUGAUUGUAGGGGUGGUGGUCAAGGUGGUUUUGGUGGUGACAGGCGCAGAGGUAAC
UAUGGUUCUGGUCCAGACAGAAACUACCAUGGUGGAAACCGUUCACGUCCCUACUGAAUC
UCAGCCAGACAAUCUAUGUACUAAAAACAUGUGGUGGGAGGGUUUUUAUAUUUAGUUCUG
UUCCAUGGUAUACUCCGUUAGCUGGAGACUAAGAGGUAGGUUGUUCACUUACUCCGAGCA
AUACCCUUUUUCUCCUUGCUGUUUGCUACUUAGAGGGGUUUGCCAGGUUGAAGAUUUGAU
UAAUAUUAAUAUGAACUAUGUGAAUGUUUUUAUAGAGGCAAAUGGAUGGUUCUGCAAAAU
GCUGCUAAGGUAGGUUUGAGAUGUUCAGGUGAGUUACUUCUUUGAAAAAACUAACAUACU
CCAUUAAUUCAAGUUGGUUGAUACUGUUUUUGAGAGUGUGCGUUCGCACACGCUGGCAUC
UUCACAUGAUGCCAAAUUUAAUGUUUAGGUGCAUCUAGAUGGCGUGGCACAAAAAGUUCC
AAGCUAUGUUGUCAUUUUUAUGGUUACUGGCUAGUAUCCAGGUCAGAAAUGGCCAUCUAG
UUUGGAAUCAGUCUUUUUUAAAGGAUCUUUUAUCUUUUGAGAUUGCUAGAGCUGGGUCCU
CAAUUCGGUGGUGUUCUUGGUUGAGUAAAGAAUCACUGUGGUUUUGCUACUUUUAGAAGU
UUAGAGUGGAUUGAAAAAUUUCGAGAUCGGUAAUUGUUUCAGUUGUAGGGAUAUCUCGCU
CCCCCUAUACACACUUCACCUUUUGGUUUUACAUAACAUAAAAUUGUGGUAUGAUGGAAU
GUUUGUUGACCGAGCUUUCCCUAGUCACAUUGGUAUUGACUUGGAAACUUAUGGCGCCUA
AGCAGAAAAAAUAGGAUGUUAUAGCUUUGUCUUUUUGAUUAAGACAUUUAGCUGGAGGAG
CUAUUUGAUUUUCCCAAGGGCACCUACACAACAUCUUGAGCGAAUCCACGACCUCAGAAG
CCUUCGAAGAAGCAUGAACCAAGGAGGUGUUGACGCCCCUUCUGCUAAACUGUGCUAUUG
AAUGCCCCCAGCUAUAGGGUCCGAUAUAUGAUUAGUGGCCAAUUCUAUCAAAAUGUACUU
UGCAGUUGUUUCUUUUGAGAAUAAGAUGGGUGUCGAUUGGUCAAUGAAAUAGGAGCACAC
GAUUUCUUGGAUAGGAGUCAUCCGUUAUUGAGAUCUCUGUUUUGUUUUGUAAUAUUGGCG
AUUUUGACAAACCUCUAUUAAACAAUAGGUGCUGCAUCCUCAUUUUUUUCUGUUUGUGAA
CGGUGCGAUUUCGUUCAAAGGAUCAUACAGACACAAGCUAAGGGGAGUUUCUAUAUGCUU
UUGAAAUUCAUGUUUACUAUCUUUAUGACUUUCAGUAUAAGGGUAGUAUCCACAUUGAUU
UUUCACUUUGAAGUUGUGAUGACUCUUACUUGUGUUUACCCCUUAGGUUUUUUUCUUGAU
UCUGUAGUAGCAUUUGUCUAUGAUGCAGGAUCAAGCACUUAUACUACAUUACUAUUUGGA
UUUUGGUGCAAAAUGAUCAUAAAAUCUUACAACAAAACAGAUUGAGAUAUUCUCGCCCUU
CAAUUGUGCACCAAAUGGUUGAUAGAUGAAAUCGUUGAAGCCUAAUGGUGGUAAGGGUAA
UGCCCCUUUUCCCUUUUGAUGACUCUUGGUGUAGCUUAAAUUUUUCGAUGUGGAUUAAAG
GGGCUGAGGGGG

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 [-626.91] kcal/mol.

2. The frequency of mfe structure in ensemble 9.16761e-30.

3. The ensemble diversity 661.22.

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