lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-630.00) is given below.

1. Sequence-
CUUAUCUUGGCUGCUACUCCAAAAUAAUAGAUUUGGCCCAUUUUCAAUUGACAUUAACAU
AUUCAAGGGUUGCUUUCUUCACUUGUGGGCUUUGGCCCAUUAGACCUUUGGCCCUUUUGU
GGUCUUCAGCCUUCAAAGGCUUGGCAAGAGAAGAGAGUCCAAAUAGACCCGGAUGAGGGG
AUUUUUAUGCAAAGAAAAGAUAAAGGAUUAGGAAUCAAUCGUAGAGAAGACUCAAAAUAA
AACAGUAAUUCAAACAAAAGAACAAAAAAACAAAAAAACAUUGUGACCAACAUAACUUUA
UCACUUCAGAGGGAACACAUACACAAAGGACAGCUCCCUAAACAGUCAUGAUAAAGCAAA
ACAAACUUGCCACAACAAACUAAUAGACAUUUCCUGACCUCUGCUUGCAAAAUAACCUCA
ACAAUAUUUACAACUGAAAGAAAUUAAUCCUGCCCAGAUUUCAGAACCAAGCCUAGGUAU
CAACCUUAAGAGGGUCUAAUCUUUCUCCUAAUUCAUGUGAUCGCAGAAAAAGGAGCCAAU
AGAAUGUAAAUGAAAGAAGAGAGCAAAUUCUUACUUACACAUAAUGAACAAGAUACAGGA
AAACCAAACCAGGCAAGCGGGUGUCUUUAUACUCUACUCAAACAACAUAUCAGGAAAAGC
AUUUCAGUUUAACCUAUCAGCCAAUCACAGAUAUCAAGACCCUCAUAACCUUUCACUCCC
UCCUUUAGGAUAUAAAUGACUAAGGAGACAAGGGCAGGGCUUGAGAAGGGGAACAACUUC
UCACGAAUGAACAAUCUAAACAAAUAGAUUUUAGGCAUGCUUUUAUUCAGUACAUAAAAA
ACAUGUCACAUAGUUUUAGUAACUAGGUUCAGCAUAUCAAUCCCUCCUUUAAGAAGAAAA
UGAAGCUCAAAUAUCUAGACAAUACCUCAAACCACAUUCUUGAACCCCACAAGCUGAUUC
UAUACCAAACAGCAACCAGGUCCUUAAACACGCUAUACAACAACGAAGACACUACUCUAU
CACACAAUAUAGUCAUCAACUUGAAGAAACAAGGAGUCUGAAGACACAAUCAGGAAACAU
AUAUAUUAAGAUCUGGCAAUUAUAAAAUCGCCUAAUUCAUAUCAGAUCUUAGUGUUCAUG
AACUAAAGCCAAGGCUACCAGGACCUAAACGUGUUACUAUAUUGAUUUUUAGGCUCCAAA
CUAACUAAUUAAUGCAAGUUCAAGCAUUCCAUAAUAUAUGCAACAGCCAGCCCCUUAAAA
GACCAAGGAAGACUUUUAUUUUUAAACAUGACAAUCAGGAAAUGGGCAACUAGUCGCACC
AGAUUUCUACUCUAGUCACACAACUGGGAAACUUAGUCAUUUGAGCCUUAAGCUGACCAU
CAAACAUGAUGAUGCCUCAGAAGUUAAUGAUCUUUCACUUAAAAGAUACCAACUUUAACA
CACAACCAGCAAUGAACGGCAACAAAUGGAUCUUACAUGAGACACUAAAUUUUUUUGACA
UACAAUAGGCUCAACUCACUGUUGAUCCUAAAUUUUUUUGACAUACAAUAGGCUCAACUC
ACUGUUGAUCCUUCAUGCCCCAUUCUUAAACAAGAAACAAUAUGAUCACGGCAGGUCUUU
UAAAAACAAAAUACGUACUGAUUCUAAUCAUCAAGAAAAUGCAUGUUUAAAUCAAGAAAU
AAUGAUUUAACUAGUUAGGUAUCCUAAAACAUGCCAUUCCUAUAUAUUUCACAUAAAACU
AUUCCUUUUAGGUAAUCCUAAAUUACUAUUUACCAAAGCAAGGAACCCAUGACCAAGAAC
UUGCCACAAUAGCUCAGAAAGCAAUCAAAGUUGAGAUUUUUAGCCAUUUUCAUUUAAAAC
AGAGAACUUCACAUUAUGUUUAGCUAACACGUCAUAAAACUCAAACUAGGAUAGCCUUGU
UAUUUAUCCGAACCAUGAAGAAAAUGAGUGAAAAAGAUGAGUGUAUUGCCUGUUUGGGUA
CAGGAACCGAGAUUUGACAAACUUGAGAGGAUUUCUACUCUUCCAAAAGCCCUGAUUUUA
GCUCUUUUAGGCUUCUUUUUGGUUCUUUAAAGGAUAGAGGAAGUGAGACUCAGAUUUGAA
CUAAGAUCAGGUGAAAAGCGAUUCCAACAACGCCAUGGCUGGAAAAACCACAAAAUUGGA
GUAUGCCCCGCCAAGAUACGAGUCGGAUGACCUCAAACGCCUGAGUACUCAGCUCAGCAU
GGAAUAACUAUUGCCUCUUUCAAUCCCCAAUUGUACUUACCCCCACAAUGUUCGCCAUCC
UCACUUUGAAACGAUUUGCGACAGACAACCAUCCAAACAAGCUCUUGAUAUCACUCCUUC
GGUUAACAAAGGAUGAAAGGGUUGUUGAGGUUACAUAAUAAUAGAGAAAUCAUCGGUUAA
UGCAGAGAGGGGCAAUCACCCUUUCAAUGAAAAAUCCCUAAACUCAUUCUUUCUCUCCCA
AUCCUCUCUUAAUAAUACUCAUAAAGGGAUAACUUGGGCUUCAAAGGCAGAGAAAUUGGG
GGAGAACCAGAGAUAAGAGUGGAGAGGUGUCGAAAUCACACUCCAUUCCUCCAAGAAAUC
CGAAAAUCCAAUGGCUCAGAUCAUUCUACGGUUUCAAAUUCAAAUUCGAAUUUGGGGAUU
UAUAUCCCAACCAAAAGGAAUUUGACAAAUCCUGUACUUUCAGUAUGAGAAUAAUGGGAU
AAGGAACGAGGUUGCCGUUUGAGAGAAUCCAAGGAGUAUUCUAGAAGGUCCAGCUCAUCC
AAUUCAUACAGAAAUGGAGAGAUUAACGAUGACCAAUGUUUGGCAAAGAUCCGUUGUCGU
UUGAAGGAGAAAUCAGAGAUGUUUGAGGUCGUUUUGAGCUUUUGUUGAGAGACAGUGGAU
GGAGCGUACUGAGCUUUGAG

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 [-682.86] kcal/mol.

2. The frequency of mfe structure in ensemble 5.68828e-38.

3. The ensemble diversity 687.38.

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