lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-639.64) is given below.

1. Sequence-
CCCGGCAUGAGGACUAGUCCGGCCCCAAGGUGAAACUGUACAAGGGGUCUGGGAAACCAU
AUAUGGAUAGUAUUUUCCAUCUAGUACAUAAAUUAGUGCAAAAUAAUCAUCUCCGUUGGA
UUGAAUUGUAGAAGAGAUUACAAGAUUCGUUGGCUUUCUUAAAAAAAUAUGGGGCAGCAA
AAAGGGGUUGAAAUGGUUCUCAAUGGAUUGAAAUAACUUUUAAUGAUUUUAUUAAGCAUU
GGAGGGCUUCAAAUAGCCAAUAACAAAGAUCUGCAUAAUUUGAAUUUCAAAAAUCACCUA
AAAUAUUUUAACAACAAAAACAACCUAAUCUAUAAUUUGAAAUUCAAAUUCACCUUAAAU
CUAAAUAACUUAUUAGCUAAAAAAAUUGCUGCAAUAACUAAAUGCAAAUCUCAACACUCC
UCCUUUGCUUUAGUUACUGCAAUUAUAAGAAAGUUGUUCCUCCUCAAUUUCUGCUUUUGU
GUUGCUUCUACUUGAUCUUUUUAAAUUUCUUUUGCACUUGCACAAAAAUCUUGCUCUUCU
UAUUUCUUUUUCUUUAGGUUUUGUGCUUAGAAAACACCUUCAAUAAUAUUAUCUUGUUUG
AAAGUGCUUUCAUUUGGAUAAUUGUAGCAUUUACAAAAUAUUUUUGUAAGGAUUUUUCCU
CCAUUACAGCAUCAUAUAAAGCACUGGUUAUAAAAUAGGGUUCAUUUUCACCGACCAAAA
AAUUUUUGGAAAGAGAAAUUGUUGCUUUUCAUUUUUAAAAAAUAGCCCUGAGGGUUAAAA
GGGUAGCCCUAACAGGUUAAAAAUUGUAGGUACUGCUGGAAAGAAUUCAAAGAUCCCGUA
AGAUUAUUGAAGCUCUUGAUACUACUGUUGGUCUUUUUUAAAAAGAUGGGGCAGCUAAAA
GGGGUUAAAAUGUCUCUCAAGCAAUUGAAAUAACUUUCAAUAAUUUUAUUAAGCAUUGGG
GUUUUAAAUAGCCAAUAACAAAUACAUCAACAUACCCAAUAUAUUCCCACACCCGUGGGA
UCUGGGGAGGAUAGAAUGUACGCAGUCCAUACCACUACCUAGGUCAGGUAGAGAGGCACC
AACAUAACAUGCAUGGCUGAUAAUUAGAACAAAUAGGGAAAACGUCGAAAUAUGUACUUG
UGACAGGUGUGUGUGUAUAGAUAUAUCGCCUAAUUCAUUUCCAAUGGACACAGAUACCAG
CAAACAACAACAUACCUAGUAUAAACCUACAAAGUGGGGUCUAUGGAGGGCAGAGUGUAC
ACAAACCUUACCCCUACUUCAGAAGUAGAGAGGUUGUUUCAAAAAACCCUCGGCUCAAGG
AAAAAAUAGUCCAAAGCAGCUCGAAAAUAAUGAGUAACAGAAGUACAAGAAGUAGCAGAU
AGUAACAAAAAGAGCAACUACCACAUGUAAUAUGAUAGUCGAAGUACAACGGAAAAUAAU
AAUAGAAAUUUAAGGACCCAAAACCACAGGAGCCGUACAACUACUAUUAUGGAGGGAUAA
GAAGACUAUAAUAAGGUCCCAAUUAGCAAAUCUGAAAAAAGCGAAUUCCUCAAAGGCAAA
CAGCAACUCCCAACCCUAAACAUUCAGCAAAAUGAGUAUACAGGAAGCCAAUAGAGGGAA
AUAAAUUCAGGAAAAAGAAAAGGAAGGUAUAAUUUGAGAGCAUGAACCCCAAAAUGUGAU
AUGUACUACAAGAUAUUAGAAAGAAAAUGAAGGCAAACCCCAAAACAUAAUGCACACAGG
AGAUACAAUGCCGAAAUACAAUUUGUGAUGGCCUGCACACGACAAUCUAAAAUUGGUUCC
UGUUCUUCUUAUUCUCCAAUCAUGGGCAAAACUAAGAGACAAUACCAGCAAUUCUACACG
AAUAGAACAUUUUAUAGCAACCCUAUAUAUCGAUGGCUGUUCCGUGAGAUCUCUUUUCAC
GUAUAAAAGGAUGCGUAAAUAAAAGAGGCUAACUGAGUCCGGUAAAUUUGCAACCUAGAA
AAAUUACUUCCACCUCUAGGAACAGGGCACACAAUAUAGGAACUGAUAAUCUUGAGCCGC
AAACGGCUAUGUAAACCAAAUGCAAGACAAUUAAAGACACUCUUUGAACCAUCACUAUCA
UACACCAAUCCAACUAAAUUAAAAAAAAAUAAUGACAUAUUAGCCCACUUAUUUUUAAGA
UAACAUCCCCAAGAUGAGCUGCCUAAAACACUGAAAUACCAACUGAAUCAGUGUUCUUCA
CAAAUUUAACUAACCAUCUACUUUCCACAAUUAUUCUUUUUUAUCAAAAAAAAAAAAAUG
GUACAUAAUUCUUUUUCUAUCCAUAACUUUCAAAUAUUAUUCUUGCUCCCACAGUCCUAA
AAUAGUUGUACAUUUCGCUUCCUCAAGAUAUAUAUAGUUAGUUUCCACACAUCCGAAAUA
AAAUAAAAAAAAAUAAAAAAAAAUAAAAAGAAGGGGAAUCUAUAUCCAAUUAAGUUCCAA
AAAUUGGUCAAACCGGUGAAAGUAGAUAGUAAACUUCUCACUUUUUUAUGCGAAGAGAGA
GGAUGGUGAAAACCCUUCGAUCAAAAGAAGGGUACACAUAUUAUCCUUUCUUUAUAAUGC
AGAAGGGUCAAGAAGGUAUUAACAAGAUCAUUACACAAAAAGGUAUUAACAAGAUCAUUA
CUGUCUGAACUGCCAAGAAAUUCAAAACCAAAUCCAUCUUUAGGUUUUGCGCCAGAAAAA
UGUAAAGAAAGUGAAAGGCAUUAAUGUCAUAAGGGUAUCAUCACAUAAGCAUCAAUUAAC
CAGAAAAAAAGGAAAUAGAAAGAAUAUUGACAAAUCGGAAUCAGGUUCUCUUUAUGCCAU
AAAAUGCAUUAACAACCCCACUUAAAAAAUCGCAUAAAGUCAUUAAAAGGGUUUAGGGUU
UUCGUCGCGUGAGAGACAAAGAGGAGAAAUUAAGGAAAUCGGGAGGACCUACAACUAGGC
UUCGCCAGAGAAGAUGAUCGCCGCAGGUAGAAAGAGUAGAAGCAAGUUCGACGGAGAAGG
AAUAGUGAGUGAGUGUGGACUUGGCUGGUCUUUGAGUGAGAGGAAAGGGUGAAGAAUUUG
AUGAAACCAAAGGUUUGU

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 [-697.24] kcal/mol.

2. The frequency of mfe structure in ensemble 2.59813e-41.

3. The ensemble diversity 664.22.

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