lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-680.20) is given below.

1. Sequence-
UGGGUGUAUUGAACUGAAUUUGCAGAUGUAAUCAUUUUUAAAGAAAGUCGUUAGCGUGUU
UUGAAAGGAAGGUACAAUUUACAGCAAAAAAACUCGUUAUAUAAUACAAAAACACUUUCG
CAAAAGUACAUUAUUAAGACUUCAUACGACGUAAAAAAAUCAAGCUACCCAAGUUAUAAC
CUAAUCAUGAAAAUUUCUUUUAACACUGAAAAGCAUUUUACUCAUAUCGCCAAUUUAAUG
ACUUGUUCCAACAUGAUGCAAAUGACCUAUAUCCAACAAUUCUGAAUUUUUAAAAUCUUU
CUUUAAAUGAGUUUAAUUAAUAAAACACCAAAGGCUACUCUCAUAUUUAGAAGAAAUUUA
GCGUAAGUCAGCAUGAUUGCCUGUUUCUCGUCGAAGAGAAUAUCAUUUCCAUAGCUUCGG
AAAAAUCGUUUAAUCAAAAGAAUCUUUCCAUUCUCAGUAAUCACGAAAUUAUUUUAUAUG
AACUUAAGAGUAAAAGAACAAUAAGAAAUUUGUACCCGUGGGGAUUCGCUUUCAGAUUAU
AUUAAGAGAAAAUACAAACAAGUAACAAACUAUACAAAAAUAAACGAGAGAAGUUAAGAA
AAGGCCUGGGAUUCAGCCUUGGGCCAAUUUAAUUCUUCACUACUCCGACAUUAGCUUCCA
UGCUUUAACUUAUUUAAGGCUUGGUUCGGACUCGAUUAGGACCAGAUAUGCAGAUGAGUA
AUUGGAGUCCAAAAUGAACUCGGACAGUUCAUGCACAGAGAAUAAUAAGGAUUAGUAUUU
UAUCAAGUACUGUCAGUCAAUUAUAUAACCAUAUGGGUAAAAAUCAAACAAUAUCUAAUG
CAUGAUUAGAUUCAAUAUCGUAAGUUCCAAACCAAUUAACACACAUUGUUUUCUUCAAUC
AAUGAUAUAAGAGUAUCUCCAAAUACUUUAGGAGUAUAAAAGAAACAUAACGAAACCACA
UAAUCAGUUUGGUAUGCAAAUAUAAUUUCCUUUUACGGUAUGGAAGUGGUUAAGCAAGCA
UGUACGCAUAUACCUCUUUUAUCAUUUUAUUUUCACAAAUCAACCAAACAGUGAAUAUGU
UGCAAGCCAGUAGAAAAUGAUUCAAAAUUAAAUUUCUUUGGACUCCAAAGGAACAGAUAG
UAUAAAGAAAACAAAAUCAAACGCACGUGCCAUGGUGAAGCUUGAUGCCGCAUUUUUUAU
UAUAAUGGAGAUAAGAAAUAAUAAACAACUAAGAGGUGGACAACAAAGCAAAAAGGGUCU
AUCAUUUAUCUUGCUAAUCAUUUUUUUAGUGAAGUUGUCAUGAGAUAUUUGAACCAAAUA
CGCCCCACACAGUUCACAAUUUACUAGCAUGAAGACAUGAGGGCUCUAAUAACUAUACAU
ACUUCAAUUUGAAUAAAUUCACAGAAAAAAUUUUCACUAAGCAGAAUUUAUAAUAAACUG
UAGAUAGUUAUUCGUGCUAUUAACCAAAAUCCACUUUACACAUGCUUUCAGUGAGAAUAU
UUACUUAAGUUUCCAAAUACCCGGCAGGGGCCCUAGAACCUAUAAACCUUUAUACACAAC
AAUCAGCAUACAGUGGUCAAAAAGGCAAAAUCUCAAUUAUAUGGGAUUAACAACGUCACA
AAAGAGACACCGUCAUUCGGUUAUAUAUUCUUUCAUAUGCAGUAUCAUUUAGGCAGUAAA
AUUUCAAUCAAAACAAGCUUUAACUAAAGUAUAAGCUGCUAAAUAAUUUUCUUUGUGACU
ACACAAUCAUACAGUAAAUAGUCUACCUUAAGACUUUUUAUUCCAUUCCAGGCAAGUCAA
GACAUGUUUCAACGACAGAUUAUGAACAUUUCACAAAUACUUAAAACAUUUUUCAAGCUU
UUCAAGCAUGCAUGAGCAGAUUUUAGACUCUUGCAGGGACAACGAAGAUAAUGCCAAGAG
CCAAGUAUUGAAGUAAGUUCCAUUUUGGUAAGAAAACAAAGAAACCAAGAAUAGAGCUAU
AACAGCUUAAGACCCUGACAGGUUACUGUAUACGAGUAUCCAGUAACUUACUUUCAUAUA
AAACUAUAUUUUCAAUAAGGAACAGUCUAUUAUACCAUUUAUUUCACAGUUCAGACACAG
ACAAAAGAAUCAAGAAGCAUCUGAAUCAAUUUUAAGCCUCGAGCAAAGCUUGAUCUAAAC
AGAACUACGAAGUAUAUCAUUAAUUAGAGACUUCCAAUAUUCCUUUCAAAACCAUACUCU
UAAAGAAAAAUAUUUAUAUCACCAUGCUCAAACCGAAUAUUUAAUCAAGAACUGAUUUUU
AUCUUUUAUUACAUGUACCUUUUAGAAUCAAAAGUCAACCUUGUUGUGUGCAACAUUCAC
AAUAUAAUACAUCCCCAACUGUUAUACUAUACAAAGCAAGACUCUUGAAAGAACCUGUUA
GCUUAAAUCAUGUCGCUCCACAUAAGACCAUAAACAUGCUGCUGUAUACAAGUAUUCAGC
CACCUAUUUUCAUAUGGACUACACUCAUUUUCCACUUCACAAAACUAUAAUUUAUCUUAU
UUCAUCUUACUCAUACUGUUUAUUAAUACCAACAAAAACAAAUGCUAAUAUCUUAAAUCU
GUAAAUAUCCUAAUCACCGAAUCAUUUAGCACCAUACUCAUCAGUCUCAGAAUCCAACAA
ACAGCAACAAACUAUACAAGAUUUCAUCAAAGUGACCAAAAAAUGCAUCCACAAAAAAUC
AAAUUUUAUCUUCUCCUUUUGAACAAAACCAACUGAUAGAAAUGAAAGACAUACAAAAGG
CUCAAAUGCUACAAAUUACAAGAGGUCAAGUUCUAACAUGAGUAGUGCAAGCAAAACCUA
CUAAACCUAAAACAGAAUGGACGCACAUCAUGGCCUCUCAAAAGAUGCUCUCAAAUCAAU
CACAAAUUAUGGUUUCAAAAAACUACUAAUCACUGGACAUUAUCUAAAUAUUAUACAAAG
UCAGCGAAUUUUACUCAAAUACCCAUAUUUAUUAUGCACUGAAACAGUAGCUAAAAUGGA
CAGCGCUCAACAGUUAUUGAAUCAAUAAAAAGAAAAGCAGAAUGAGGUUUUCGUUUUUAC
CUUGUUGGAAGCAGCAAACUGGGACCAAACUGGGACAAAAAUAAAUUGAGGUGAUUUCCA
CAACUUUCGAAACAUUUUGCAGAACUAAACCUCACAAAUCUUUAACCCGUAUAGACGCAA
GGAAAGGCCCUUUAAAGAGACGCCGCCGUAGGGGUUUAAGAUCACUCUGAUUUUACCUCG
UCGAUAAUAAACGUUUAUUCUUAACUAGAAAAAAAAAUUAAAUCUAGGCUAUAACCUUAA
GAAUUUUUACCGGAAUCUUUAAAUGCCUAAACCCUAGCCGCCUCAAAAAACCCAUCAUUC
UUGCUACUCAGUGAAUAAAUAGGGUAUUUAAAGAAGGCGAAUUAGGGAACGAUUUGGAAG
GGGAGGAAUUAGGGAUUUCGAAUCUCAAACGGGAUUCCUACAAUCAACAAUCAGAAACCA
ACAAGCAAGGUACUAUUUGCGGAAAAAUAGGAAUGUUACCGUUCAAGGGCCACCUGGACG
AUUCUAGAUGCUUCUUGAGAUGGACAGCUCAACUUUGAAGGAAAAUUUGACGAAAUUUGG
AAACGUUAGAAGCAUCUUUGAAGAUUUCGUCGUUUGCAGCUUGCGAGAGAAUCGUUUUGG
GGGUAUAGUUGACGGCGGUUUGGAUGGUUUGCUGCUGUCGUUGUUGAAGUUAGAGAGACG
AAGAGAGAGAGA

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 [-755.77] kcal/mol.

2. The frequency of mfe structure in ensemble 5.61863e-54.

3. The ensemble diversity 855.12.

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