lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-424.00) is given below.

1. Sequence-
UUUUUUUUCAACAAUAAAGAAAUAGUUACUUUCAUAUCAUAUUCGUUUCAAAGUUCAUAU
CAAAUCGUUCAAUGCUAAAAAUCGAUUCAGGUAAAUUAUCAACACUCAAGUAGAGGAAAA
UUAAGUCAAUCAUGUCAAGAGAGGACAAAGAAAGAAGAGAUAGCCAUAGGUUUCAAUUGU
UUAUAAAUGAUGCACCGGAACUACCAACCUUAGGCCAAUCAUCCAAUGGACUGGUGCAGC
CUUGCAUAAGAUCCACAAUGGCUAUUUGUCCUCUGAAAUAGAAAAACUUUCCCAUACAUU
ACCAAACACAAACAAUAUUAAUCAUGAUAUAAUAGUCGAAAUAAUAAAUCAUGGUAUAGU
AGCCGAAAACCUUUUUUCAAAAUUGUCAUUCAGCAAUAGAGGUAAUUCCAAAAUCAUUGU
UCAAUUUAUAAACCAUGUUUGUCAUUGAAUCAUGUUUCAAAUGAGUGGCUCAAUCAUCCA
GAAGAAAACAUGUUAAAGGUCAUUACUCUAAAUGCAAUUUCAACAGUCUCAUUCAUAGGG
AAUAAAGCACGUUUGUAUACAUAUAUUACAAUAUAAAAUCAAAUGAUGGAAGGUUCAAUG
UGAGUGUUACAGGUGUCAAAUGAUUGAGUGGACUGAAUUUGGUUGGUCAAAAUGGGUUGA
GUUAAUAAGUAGGUAGGUAAUUAACCCACUCAAAAGCUACUUAGGCUGAAAUGCAAGUCA
UAAUCCAACCGAUCAAUUUAUUACCUCGUUUGUUCUUUUAUAAAUUUUUAGUAUCUUAAA
AGUACAUUUAUUUUCUUUAAUAUGGUUAUAAUAACAUAUCAAAUUAAAAAAAAAUAUCUU
UUUAAAAAUAUUUUGACAAGAUUCUCCAAAAGCAAUUUGGGUACAUAUCAACCCGAUUUA
UAAUUAGCUAAAAUGGAUUGAACUAAUAAAUGAUGGAUUAAUACCCCAAACUUAAACAAA
UUAAGUAGAUUAGAUUGAUUUUGUCAUCCUUAUCAAACUAGUCACACGCAUAAAAUCUUA
UUCAAACCUAAUGGUCAAAAGAUGUUCGAAAAGAGCCAUACCUCAAAUCUGGCGACAAAG
AUCCUAAAAGUGCUCAACACGUUCAAUGGCAGCUCUAUAAUUAAUUGCGAUGAUACAGUU
UAAAACUUUGAUUGAAUUCCAUAAGUUUCCACCCUCUUAUAAAAAUCUAGGACUAUAGGA
CAAAGUUCAUAUUGUAAGAUUUUGAGAAUCACCCAACAACUAUGGUGCCCUUCAGUAGGC
UACACAAACCCCAAAUUAUCUUUCUAAUAGCUAUAAUUAAGUAGGGGCUUAAACUCACGA
AUAACUCCCAAAAAAUCUUCUUCUAGUGAUUUCGCAUCAAGCUCCUUCAAUCGAUAGAUU
AGGAUGAGAAUUUGUACUGUAAUUCUUGUUAAAUCAAUAUGAUAACUAUGGCACUUGAGU
AGGAACUAACAUUAGAUAAUUAGAGGAUGCCUCUGAAUGUUUUCUCUCACAAAAGUUCAU
CCAAAGCAAGGUGGAAUGAGAAUUCUGAGCUAAACUCGUAUUUAUAAACAACUGGCCGAA
UUACCUAAAAUGCGAUAAUCUGUGGCCCACACCAUCCAUCACGUACUAUGAUCAGUGUGC
GGCAACCUGCAUAUCACCAAAAUUUGGCACUAUAGACAAUGGGUCAUACCCUCCAUUGCG
UGCUAUGAUCAACGCACCACACUAAAGUUUGAUCCUAAGUCUGACUUCAAUAAAAUGUCU
AUAAUAUUUUUCUACAGAGCUCGAAUUAUCUGUCCAAUGAUUGAAUAUAUUUAAGAAUCA
UGAAAUUAAAAGUCAAGAAUCUUUAUCACAAUAACACUGGAUAGAAAAAGUACUUGAACC
UAAAUAUUGGGGACGCGGAUUCACAACUAGAGUAGACUUGCUUAAUUAUUUUAUAAGAAC
UGAUGAACACAUUCUUAUUAAUCCCAAUUCCAUUAACAUAUGCAUUAGAUUAAAUUGAGU
AGGUGAAUAGACACUCGAAAAAUUCUCAUGAGCAACAUUAACCUAGUCAACCACUAUAUC
AGAUAAUUAAAAAUGACAAUUUAAGUUAUGAUGAAUAUGCAGUGUGUUGUAUCAUAGAGC
AUUUCAAUAGUUGCCCCAAGUCAUUUAUGACUUGCUGGGACCAACGGUUCGGAUCCCCGG
CUACUCGGUUGAGAAU

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 [-466.62] kcal/mol.

2. The frequency of mfe structure in ensemble 9.26705e-31.

3. The ensemble diversity 527.64.

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