lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-539.50) is given below.

1. Sequence-
GAAAAUAGCGGAUUAUACUGGCGCGCAAAAUGUGUUAUAUCCAGACACUAUCUGGACUGC
AGAAAUUAAGACCGACUAAUGAUCUGAUGUAAAAGAGCUGGUAGUGUCGUCUGCUAUUUG
CUGCAACUGGAGUUUCAACUGUGAAGACCUCUUUAAAUGUGUGGUAGUUUGUACUUUGUG
ACAAAAUAAAUUUGAGGAUGUUUCAGUUUUGUGUAAGUAUGAAUGGAAAGAAUGGUUGGA
AAGUCAAAGUUAAGGAACUUUGUACCACAUUGGUAGAAUAGAGAGAAGUGGGACACUUAU
AUAGAAAAGUGUUCCUUGUAGGUUGUAAAUUGUUGAUAAACCUAUAUUACAUGGUAUAAC
CUCGCGUACGUGCACGUAGGGAGGGGUGCAAAUCCAAGGUUGUGCGGAAGUCAAAAUAGC
UUGACUCGUGUGUAGGCGCGACCUGCGGACCGAAACAAGGGGCCUGAUCAACCUCACGUU
UUGCCACUGCUUACCUUUAGAAAUUUCAAAUGACUUUUUGCAUUCUUGAGGCAUGCCAAA
AAUCAUGCAGAAUUCAUUGAAUCCAUCUCAAGAGUUUGAGUUAGUGGAUAUGAAUUCUAA
UAUAAUAUAAUGAGGGGUUUUGAAGGGUCUCCAACCAGACCAAAAGUCACACACUCAACU
AUAAAUACCAAAUCUAUUUUCCAUAAAAAAUACACGAAAAUUCUGAAUUAAUUUUCUUUC
UUUCUUGCUGUGUUCAUGUAUUUCUUUUCAGUUCGUUGGUGAAGUUGUUUCAGUGCAAAA
CAGGCUUCACGUUUUUUCGUUGUAUCUGGGAAAUAGACGCUGUCAAACCUCUAGCACUAU
CGGUAAGGGGCGAAUCUGUUUUAAGGAAAUUGUGUUGAACACAAGCCUCGAAAUUUUUUU
UUCACUACUUUUGUUUGUCUUACUAUUAUUAACAUGAGUAAAUUUUGACCCCUCUUGAUU
CUAGAUUGUGAAAUAUCAGAUUGUGUUUCCAGUCGGGAUGUUGGCCAUUUUAGGCGAUUG
ACUUUUGUGCGUGAAAAUAUAAAAUAAAAUAAUUUUUGGUCAUUUGGUUUUGCCUAUUCU
UGAUUGAGUGACCGUAAAAUGGUUUGAAUAAGUCCUCAUAAAGCUUAAGAUUUUAAGUAU
GGUUGCUGCCUAUUGUGAAGUCUUUGUAAUGCUAAUUGGAAUGUUCAACAUCGUUGUAAC
UGUUUUAAGUAUUGUUUGUGCUUGUCUUUGCGUAUACAUUAAUAUCGGCAGUUCGCACAU
UAGCAUUGAAAAGGAUUCCAAAAGGCUUAAAACUUUAUAUGUUUGGCUGUCGGUCAUGGG
AUCGUCUUUACCUCCUUUCGUCUUGAGCACUUGACAUGCACCAAUUGUUGGUUUAUUAUG
CUAGCUGUUUACUUAAGUAGGAUUUUCAACUUAUAACUAAGGAAGCAAGCAAGUCAGUUA
AAUUUUAAGCUUUGAAAUGUAAUUCACCAUAUGUUUGAAAAUCUCUGUUUUGUCUGAUUU
CAUGAGUGUAGAAGUAUUAAUUUAAGUCUCAAAUAUGUCUCAUCUUAUCUUUUCUCGACA
UGUAGGUUCUGUGAUGCUUCCCUUUUACUUGAAUUUAUUGCCUUCUUAGUAGCUCCUUGA
UAUGUUUUAAAUUGCUGAAAUUCUUAAAUCCUUGUGUUGUAAUAAAGUCAUUUUAAUAUU
CGACUUCUCUGUUCCAUCAAUUAGUGUGUUAAGUUUGUUCGAAGGCAGUCCAAGAUGUGU
UGGACGGUUGUUGACGACCAAAGUUAUAUGCGAAAGUUAAUUUCACUUGUCCUUUUGGCC
AUGAAUACCAUUUUAUUUAAAUGUUUGAUUUUUUCACUUGAUUUUGUCUAUAGGAACCAU
UAAGAAGAAAUGCCUGAAUCCCGGACAGAUCAUUUAUGUAUAGGUAUAAGAUGCAUUUGU
CACCCUCGUCAAUUUAGAUCUUGCCAUUAGGGUUAAAUACGUGAAUGAAUUUCCCUCCCU
UUAUCCCAUUUCAUAAGAAGAAGAGGACAAUUUCCCUCCCUUUAUCCCAUUCCUUUGCUU
CUAAUGUACAAAAAACAAAAGAGUAAUCCAAUUUCUAUGAUCAUGUUUGAUGUGGUGGUG
GUCCUAAACUUUCUGUUUUCGCAAUAUGUACUUUUAAAUCGCUAAACUUAAAGUCUUUUG
CUUUCAAUUUAUUUUCUUGAAAUCAUUCAAACGAAUACUAAUCCUUCACUCUUAUUUUUC
AUUGCAUGAACCACUCGAGAUGAGUCCAAAGGGACUUGACACACCUCUUGCAUGCUUCUC
CGAGUCCACCUUAUAUGUUAAUUGCUUGAUUUAUGAAGUGUUACUAAUUAAUUUUUUUUU
CCUCUCUUACUAACUUGGAUGAAUCCC

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 [-586.79] kcal/mol.

2. The frequency of mfe structure in ensemble 4.77536e-34.

3. The ensemble diversity 734.70.

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