lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-367.18) is given below.

1. Sequence-
CCCGUAUCUGUCAAGACCCAAAAUUUAGAUCGUAAUAGCGUCUACCACCCUCCGGUAGAA
AAACUGAAUCCCUCGACCCAGAGCCACAAACAAUGGGCUGAUAACAAAUAACCACCAGAA
AUAAAGCAGUACAGAGUAGGAUGAAGAAAUAUAUAUAUAACAACAAAACAUAUUCAACAC
CUCCCAAGACAAGUGACUGUGAUAAAAUGGAGCUAACUACAUCAGAGUAAUCAAAAGAUA
AUAUAUACAACUGCCCCAACAGGAGGUAAAUACAAACACAAUCUGCCCUGAACAGAUAAG
ACAUAAACCCAACACUACUGGAGAACAAGCUCAGCCCGAAUGCUGGAGCUUACCUUAACC
UCCGAAAUCAACCUGCCCCUCUAUUCAACACGAUCUCGUCUCCUGCAAAGGCCCACGCUA
GUAUCUACACCACGAAAAUGGUACAGAAGUAUAGGAUGAGUACCAAAACACUAGGUACCC
AGCAGGCAUCAUCGGCGAUCGAGCUCAAUCAAAUACAAGCAAGAACAACAAAUAGGUAAA
ACAUGUCAGAAGAAAACAAGUAAAAACAACACAGAAAAAAUAAAGCAUAACAAUACAGAA
AUCAACUAAAAACAACUAACACGUGCACAAACCCACGGAAGCGUAGCUGAUAUCCAACUC
AACUCAACCGAUAAAUAGAACGAGUAUGAAUAAGUAAAAACAAAAAUCCAAGCCGAAAGG
AAAACAAUUAACAGAUAAACUCCGGUGGUGCCCAUCCCACCACUUGAUACAUACAGAAGA
GAAAAACAUACAAAACCUUCCUGACACCUCAUUCUGCUGGUAGGCACAAACAAGAAUGUA
AAACCAAGCAUGACUACCCCAGUCAGCCCGCCAGGUACAAACGCGAUAAAAGGAUGAUGC
AAGAGGGUGGAACUGUACUAACACACUCACUAGGACCCGCCUUCUGGGAGCCCCGCUCCA
UAGGUCCACACCUCUUUAGUUCCAAUAGAAGGGUCCGAGCCUCCUUAUCAAAUGCAGGAU
UCACUCUCUGUUAGUGCCAAUCAAUAGAGUCCCCAAACUUUAGUGUCAAUCAAUGGAGUU
CCUAACCUCAAUCCAAACAACCAUGAUAUAACCCCGUAACAUACAUAAUAUAUGAAAAUC
AAGUUUUGGUUAUUUAUUUAUGAAAAUAGCCCACACCAUCUCGCGGUCGUGAGAGAUCAA
GUUAUAAAACUCUGCUUUCAGUGUUAGUUUCAAAAAAUCACUGUUAUAUUAUCCUUUAAC
CCUCCUCGAGUAGUAAAUAACAUAGCAGACCCCGCCCAAUCAACCUCACCACAGUAUGCA
UGUCUGCGAAAACAACCAAGGCAAAUAGAAAGAGCGCUCAAAGUCUAGAAAGGCCAGAAA
CCACCAGCUAAGCACACAUCUCACUCGACCAGCUAUCAAUAACGCAGCAUCAAUGCUACA
ACCACACAGCUUCCCCCGACAGGCGGGGUACACUAAACGCAGCCUACACUAGCAACGACC
CUCACACGGGCCCCAAAAGGGUAAACAAGCGCAGAAAAAUAAAAGAAACGGUAUAUCAAC
AGCUUGUCCAGCCUACCAACUACUUGAAAUCCAAUAACCAUUCAAUAUGAACCCAGUCUA
AGAAUUAAGUAAAAACCUAAUCCACCUGGACGCUGGUAAAUAGCUCCCGUAAGUCGCAUA
UACAACCGGAACAACCUCAGAAACGCCCGAAACAACCUCAAAACGCAGUAAAACGAACAC
CCAAAUACUUCCAGAGCAACCACCAGCAAUACCCAACAAAUCCCCAAGAGUUAGCACCAA
GAACUGAUGAGAGAAAUGGAAUUUGUGAGAGGAAAAUGAAAUGGGAAAUGAAAUAGAUAU
GCUGGAACCUGGUAUUUAUAGGUAUUGGAAGCCUUCACCACGAUCGCGCCCAAGUGCCAC
CCAAUCGCGACUUGGCAGGGUCGAACACAGCGCGAUCAUGCAACCAUGUAAUAUGAUAGC
GAUACACAAUUUUAGAAGAAGGGCG

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 [-402.13] kcal/mol.

2. The frequency of mfe structure in ensemble 2.36046e-25.

3. The ensemble diversity 510.41.

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