lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-586.50) is given below.

1. Sequence-
UGUUAACUAUAUAAUAAUGACGCUUUUUUAUAUUCUCACAUGAGCUACAAUUUACAAAGU
CGUCAAUAGCGGAAGAAUACACUUCUAUUACAAAUAUAUGGUGUUUGAAUUGAAAUUUCA
UCUAUCAAAUCCUCACCAACAACAAGGUGAAAAUGCAAAUAGUCAACCAACUGAGCUAUU
GAGAUUCUCGACAUGGACAUUCCAAUUUUGCUCUUUCUCAGCAACUUAUCUUGAACACAA
AGCAAAACAGUUCCCCUGAUUCAUCGAAUUGCUGGUUGCAGAAGGAUAUGAAUUAUGAUC
UUUGAGUCUGACAGAUCGUGGACUGUCACCCUAGUCCCAGCCACCACUCGUUACUUCUGG
AGGCCACCGUGGUUCCAGUAGGGUUAUGUGACCUAUGAGGAGAUAAAGACAUACUUGGUU
GUACAGAAAAAUCACGCUGCGAGAAAGCUUAUGCUGAUUCGGCUUAGAUCAUACAAUGUG
AUGCAAGAAAGCUUAGAUCAUACAGUGUGAUGCAAGACAGAGAGAAGAAGAAAUACAAUU
UCUUUAUUUGGAUGGGGGAGAGAGUGAAGGCAAUGUGGAACAUGUACACGAAUCAGAUGA
GGGGAUGCUUAUCGAGGAUGCAGAAAGAUCGCACUGGAUACUUGUCACCUCCCACCAGCA
UUAUGUAUCCACUUCAUUGAUCACCAAGGUAACAACAGAUGGAAAGAAUUGAAUUUGAAC
UGGCCUUAGUUUUUUAACCCACUUCAUUGACCACUAGGUUCCGUACCAUUGGGUGCAAUA
UGUUUCUAUUUCUUAGGUGCAUAUAUUCUUCAAGUAACUCCUGUACCAAAGGCUCCUAGG
AAUAUUGUAUUAAAGUAGGCUAUGACUGACCUAGAUCCCUCCAAUCAUCCUAAAAUAUUA
GUUGUUUAAAGAAGAAUAUAAUACUAACUGAGCAUCUGAUGCACCACUUUCCAGAACGGU
GGUAUUUCUUAUUCCAUGUCCAAAUGUUCGAAAUAGAGCUAUAGAACUUGAGUUGUUUGA
UACAGCAGGGCACCUAGAGACAACAAAAUUGAAAUUAAAAACGGAGAGAAACAAUGCCAG
UCAAAUUUGCUUUUGGUUAGGCUUGAUCAGCGCGCCAAUAAGAACGCUGAUCAGCUCAUG
CCUUGGGACGGUAAGAAGGGGGAAAUAAUCUCUCUCGCACACACCCUUUCUUUCUUUAUU
AUUUUCAUUUCAUUUUUGUUACUGUUUCCUGUAAAUAAUCUGAAAUCUGAAUGAUUUUCC
AGGCAUUGCAAGGCAGCCAGAAACAACGACCAAGAGGAAGAGUGGAGAAGCAAGGACAUA
UUGAUGCUCAAUUGCAAGUCAGCUGAAAACAAGAGGCAAGAAGAAAGGUAGAUAAGGAUG
GAGCUGACAUUGAUACAGCCCAAAUAGACACUGCUAAGUUAUUAACUUAUUAAAACACGA
UCACUAAUGCAUUAAUGUUGCCAGGUUUCUCUGUAAAAUUAUGAGUGAUCUAAAAUAGGC
ACUUGCUCAUAAGUUUGUAUUCCCUCCCUGCACUGCAAAGUUCAAUUUUAUACUAGUAUG
ACACUACUCCAUCUGAAUGUACAUUGAAUUUAAUAGGCUAAAUCAUAGUAGUAUAGUUUA
UGAUUUGAGGAAUAAAUAAUUGUUAAAGUCCAGAUGAAAGUCUUUUUGGAGAAACAAAAA
CCAACCUUAACUUGGGAAAGCACCACUUUGGAUAAAUAUGGUUCUCCACAAAUUGCACCC
AAUCUUCUAUAAAAGGAAUCUUAUGCCGUUACUCUUCAGUUUUCUGAUGAAACCUAUCCA
GAAGAGGUUUCUCAAAAUUUGAGUCUCAAAUUGGAUUCUCAUUAUAGUAAUCCAAAUGAU
GCUAAAUCUUUCUUCCUUUAUUCACAUCCGAAAAUAAGAGAGGAAAAGGUAAAAGAAACU
AUGUACUAUAGUUUUCCUACUAGCAAUAUAGAGAGAUACUACUACACUAUAGGAACCAAU
ACAACAUAUGCAUUCAAGUCUCCGGCACAAACAGUAUAAACUACUUCCCUUGGAAGGAGC
UGUUAAAUAUGCAGCUUGAAAGCUAUAUUUAGGUUAUUUGGUUUCCACCCGUGAUCAAAG
AGGUCCUGUCAACAGGUUCAUCCAGCUAAAUAAACCCAAAAGUGGGUUACUCAAUAGCAA
UCAUGGUACUCAUUUAUGUCAAGACAAUAAACUAUAGGUUGACUCAAAAUGUGAGUGGAA
GGAGAGUUCGCCAAAAAAAAAAAAAAGGAACACUACAAUGAUCAAACGUUCAAAAUAUGA
UGCGUCAGAAAAAUUUCUGUUUGAUGUAGAAGAGCUAGAAAAGUUUUCAGACUGAUUUAG
UACCUACUGGCUCGUAUGCUUUCUUAUAGAUCCUCACCCUCACAUUUUGCGCAUUCACUC
CUUUAUGGUUGCUAACAUAUUUCUAUUGUCUAUCAUAAGUUACCAAAAUGACAUUUACUG
CACAGAUGCAGUUCCGACAGGAAACCACUAGCUAAAUAUUGGAACAAUGCAU

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 [-633.18] kcal/mol.

2. The frequency of mfe structure in ensemble 1.28091e-33.

3. The ensemble diversity 672.47.

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