lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-706.10) is given below.

1. Sequence-
CAUGUAAUAAAGAAAAAUUGAACAGGACAUUUAUUAAUAUGAAUUAAUCCAGACAGUAUC
AUGAAGGAAGCAUAACCCAGUUAAGAAAGCGUUGUUAUCACUUAAGGCCUAAAGCAAAAU
AUAGAGGUAAAAUGGUGCUUUAGUGAAGUCCAAACUUCUAAACCCCAACACAGGCUAAGG
CAACAUAAACUAAACAUAAACUAUCUUGCAUUUAACUCAGAGAAGCAAAGCAAAUUGAUU
ACAAGAUUUUGAGAAAAGAAGAUACCCCAGACGCAUGUAAAAUUCAGAAAGGGAACAGUA
AACAAGCUGCACCAACAUUUACAAGGACUAAAUCUAUUUUAUGGACAUAUUAUCAAUUUG
GACAGGCCAUUCAGAAUCAAUAAGAGUGAAUACCAAGUCAAUUAUGAAGAAACCACUAUA
CCAUUUCUAGCAUUUAACAUGUUAGCAGACAAUGCAAAAAUUGUAGGUGAUCAGGUGCCA
CUUAACCUGAAUCAAUUAACCAGAAGCGGUCCCAGAUUAUCAGACAGUAGUUAAAGAAGC
CAUUAAGCAGUGUAAAGAUGACCAGAUAUGAAAUAAAAAUAUAGAAUUUCUAGUAUCUCA
UGAAUCAAGCAAACUAAAACAUAUAAACCUUAACAGUGAUCAAGUAGGGAGGAGCUCAAU
ACUUAGUCAAAUAAAUUAGAUUACAUGAGUUUGGCACAUGUCAAUUGAGAGACAAAUAGG
UAGAUAAGAACACAUAGGCCACAUAUUGUCACCUUCUUUACACAGUCAACUAGUACCAGC
AUACCACAUUAUAUCCUAGUGUUACUUGGAAAUCAAGUGCACAAGUAAACUAGUCAAUGC
ACAUGUGAAUAUAUAGAAUAAAAAAGUAGGGAGGUUCCAAAAAGGUAUGAGCACUUAACU
AUUUCAAGGAUGGGCAUUGACAGUGAUGUAGUGGUAUUCACGAGGAUAUUUAACUCAUAU
UAUGACUUAGUCAAGUAUAUAUAGGUGGUAAAGUCCUUUAUGAUGUAAGUAAACAGCAAG
GAUGUCACAUUGAACCAUAUUAACUGGUCGGUAGGAGUACAUAUGUGAAAAUCACUAGGA
UACAAGCAGUAUGCUAAAGAACAACUCUUAUUCAAUUAGACAAACAUGCAGUCAUGCCUA
UUAAUAGAGAUGGUAAUAUAGGUAAGGACACUUUAAAUGUGCCAGAUACCUAGGAAUUUU
UAAACAUAAAUGGUAUAGCUCAUGAUUAAUCAGACUUAUUCUAAUCUUUGUACAGGACUG
CAUAUUAUAUUAUGCUCAUUAGAGACUUACCAAAGCAGCUUGAUCAAAAUUCAGACAUAU
AUUAGAGAUAAAGGUCAAACAUUUAAACCCACGCAGUAAGUACAGGGCAGAGAUAAAACC
AAGCAUAAGGAACAAAAGACAAUUCAGCUAUUACUUUCCUGAAUUUGCAACAACCUAAGU
CUAAAUACCUUCGUAUUUUAUGGAUAGUCAUAUCAGCUCAGUCAGCAUACAAGCAAACAU
CAUGCUAUCAAGGAUUCACUGUAUUGAAUUAUAAACACUUACUAACAAGUUCCUUUAUUG
CAUUAAACAUCAAGGGAACCACAUAUAUAGGUAAAACUGAGUAUGGAGCAGGUGGAGCUA
CUUGUAUCAAGUUUAGAUAACACAGAGCAGUUAUCAUCUCAAAACCCCAAAGAGAGUCUU
UCAUAGUAUUAAUAGACUUUAGGCUAGUAAUAUUCAAACAGAGCAAGAGUAAAGAUCAAA
CAUAAAAAGAGAAAGCUAUUAACAGUAAAUGAAAUAGGAACUUAUCUUAAUGAUCAGUAA
CACUUCCAAAUUGUGAAUAUCAGCUAUCUGAAAAGAAAUAACAAAAGUUUUGAGGCAUCA
AAUGCCCCAUGUCCCUCAACCUUUAAAAUAUUUAUACCCUUGGCUUCCUAGGUAAUGAUU
UACACCCCAUACUAAACCAUAUAACUCACCUUAUUCAUCGUCACCAGGUGUAAGCCUUUA
GACAAGUGGAACAACAUUAAAUCUUAUCACAGGCCACCCUAUGAAUCAGCUUAAACAUUU
UGACUAGAAAAGGACUCUCACGGAGCACAAAGAAGGUAAGGGACACUUUUUUAAUUUGAG
AGGAUAGGGUGGAUUGAGGGCAAUUAAUAUAGGAAUUAGAGGUGUCCAGUUGAUUACAUA
AAAAUCAGCUAAAGACAAGGGACAAAUGGCCUAGGAUUGCCUCCCUACCUCUUAAUUCUC
AUAGCAACCUUAAUGCCUUACUGCCUUUGAAAAAGGACACAUUUACUUUUAAAAAUUUGG
AAAGUAAGUCAUGAAAAAAACACAUUUGAUAACUAUUACCGCAUGAAUAAAACACAUUUG
AUAACUAUUACCGCAUAGCACAUACAGAAGAGACUGUUAGACUGUAGGAGGUGUUGAGAC
AGUGGAAAUGUAAGCUAAGGUAACAUUAUACAAAUAGUUGAGUACCAACCCAGUUAAUUC
UAAAUGAUCUUUACAACACAGGUUCAACCUUAAGCAGCGACGACAUAUUAGCAAAAAAGC
UAAGCAGCACAUCAUAAACUGGCACAUGAUAAAAUAGUCUUGAAUAUCCCUUAUAGAAAA
ACUUGACCAUCAAAUCAAAGCAAGCAACACUUACAAGCACAUCAAAUGCAUUCUUAUCAU
AAUCUAGUUUAACAUACCACAUGUUUAUCAAAUAACUAACAAAGAAUCAACAUAAAACAA
GAAGUAAAAGGGGUAAAGGAUGGUAGUAUACCUUUUUAGGGGCAGCAAACUGGAACUAUA
GAUUGAGGAAGGCUAUACCUAUUUUUUCAACAUUUUUAACAACAUUAAACCUCUCAAAUC
UCUAGUUCCCCUAUAGACACAAGGAAAGACUCUUUAGAGAAAUGUCGUAGGAACUAGAGC
ACUCUUAUUUUACCCCAUCUAAUAUAAAAUGCUUGAAACUUAAAUGAAUAUCUAAAAAAG
CUUAAAAUAUGAACCUAAAGAUCUGUUUCUUGUUGUCAUUUCGAAUAAGAACCCUAAAAC
UCUUCUUACUUUCUACAAUAUUAGUUGCUUACUGCUAUGUUAUCCGCUCUCUUACUACCA
GCUAUGUGCAACAAGGAAAGGGAAAAUGAUAUAUUGAGGACCGUGACUUGUUCAUCAAGU
GGAAAAGGAGGGGGAAACAUUAAAUCAACCAAGCUAAACCAAUUCCAACCCUUAAAUUGA
AUAAAAAAGAUCCCAACCCUUUAAGGGUCUUGCAUUUCAAUUCAAAUUAGAGUUUAGGCG
AGGGAAGACGUAAAACAUAUAAUCAUUGGCUCACAACAGUGUAUAAGUUUUCCAGAGGGG
AUAAUAAUCCCAAGAACGACACCAUAGAGAAACAUUCCUUUGAAUGAAAAAGACGAGUAC
AACUGUUCCAAGAAUGAGCGGCCACCCUUAUGCCACGAAGCCACAAGAUGAAAACAGGAG
AAGAUCGAGAACCAUCCAAAAGCUUCGAUAAAGCUUAAGAGCAAAGAGGGAACACGGGUU
AGGGUUCUCAAAGAAAGAGGGGACAAUGGGAAUUGAUUUGGAUGUUCGGG

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 [-767.16] kcal/mol.

2. The frequency of mfe structure in ensemble 9.40565e-44.

3. The ensemble diversity 886.05.

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