lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-451.07) is given below.

1. Sequence-
CAUGUUGUUUUGUUUUUUUUUUGUCCUGCUACAACACUAAUGUUAUAUGUUUAUUAUUGC
GCAGCAUACAUGCCCUUCAUGUGUCAUUCGUGCUUUAAAUCCUUCUCCACGAAAUUAUCU
UCCCCUUUUUGUUAAAAGUCAUCGAGCUCGAUGUUCUUCCAUCUCUGCGCACACACCAAA
UCAAGAGAUUCCGUCCAAGAAGUAGUUGACAAAGAGAAUCAGCUUGAUAUGGAAGAAGCC
AACAGGAUAAAGACACAAAGUUAAUCUAUACACUAUUUGACAAAGUUGUCCAUUGAGGAC
AAAUGGAGUCACAGGUGAAAGAACAAUAGGAAAAAGAUGAGAAUUGAAUCAACUUCACCA
CUAGCACAAAUCCAAGAAAGGAUAAAAGAGAGGCAGAUCAUUUGAUGGGAAAUUGAGGGC
CACCGUGUCUGGUAAAGUGACUGCACAUGAUCAUAAUUCUGCUUUGGAUCUUCCACUUGG
CCUUAUGUUUUGUUAAUAAAAUACAAGCAUCCAUCAAACGGGACAAAACAAAAUCUGGCC
AUUAGAAUUUCAUAAAACAAUAUCAAAACAAGGAAAAAGUUAACAAGGAUGGCACCUCAG
GACAAAUAAACAAGUGCAGUUUGAUACAUCUGGGGAAAAGAAGACCACAGAACAGCACUU
GCAGCGUCCUAAUAACCCCAUUUUAUGAUAGCCAACUUGCUAUAUUAACUCAUUUUUCAU
CAACAUUUUAAAAACCUAACUGAACAAGACUUAAAGUUUCAGUCUAGCAGGAUAACCCAC
CAUUCAAGUUCACAUGCACAGCCAAUCUCAGCAUCAUGACAAAGACAAAAUUGGAGUUUG
AAGACAACUUUAAGCUAAACUCUUCUUAAACUACAAUGCAAUGCCUUCGGAUGAUACGGA
AAACUUCCUCGUGAAGCCAGACGAUGCAAGUCCUUCCUUUCUUCACAAGACAAUAAAAGG
CAUCUGCACAUUAAUUACUUAUAUCAACAAAGUAGUCAACAUGGAAUCAACCUCGCCAAC
AACUUGGAAUCUAAUAUACAGCUAAAGCUGAGCACAGAAAUUCAAAUCCAAACUAGAGUU
UCUUCCUAUGCUAGAACAAGAAACUAAUCUAACUGUAUCUUUAAAUAAGGGUCAAAUGAA
AAAUAUAGCGGCAAAGUACCUGUAAAGUUGAGACACAUCAUUUCGAUAUAAGAUAACUAU
UCCUUAAAACAUAAUUGCAAAUAUUACUUCAAUAGAAACAUUUUCCAAUCAAUUAUCCAC
UUCAUAUAAAUCCAUCCAGCUUCCAUUCCAAGUGGAUCAAUGCUCAGUUGUUUAAUUCUU
CAGCAUUACUAGACAAAUACCUGAAUUGAUUGGUGCAUAGAGGAACAAAUAGUAGUACAA
CCUGCAGCAUUACCAUACAGACCGGGCUUCAUCAAUUUAAAACAAAUUCUCAGUACACAU
UGCAUGUCACAAGGAACUUCUGCCCAUUGCAGUCAUUUGACAAGGGUACAUCAAGGUACA
CGGGUACAUUACAAGGUACACGAGGGGAAGUUUUACAAUGAACUCUACAAGAUACUAGUC
UUAACAACAGUGGAACAAAUUUUUAUGUGACUGACGGAAUUCUAAAUAUCAACUCCGCCA
UUCUCCCACAGAGACUAAGACCUAGAGUAAAUAUUUGAACAAUGGAAUUUAUCCAACACG
AAAACAGAGGUUCCUCAACAGAUUGGAAAAGGUUGUAUUUAGACAGAACAAUGAACAAAU
GAUUCCAACUUUGGGCGUGCAUUCUUUCCAUAUAUAUAUAUAUAUAACAGAAUUAUCGAC
GUUAGAAGCGGCAAACAAAACACACCAUGCACUCUUUAUGGGAAAAAAAACAGGGAAAGG
UUUUUCCAUCUUUUCCCCCUUUUAGCUUUCUUUGUUGCAUAAACUUUCCGGCAUCAUUAG
CUUGAUGCACCUAAGGUUUUUUAACCAAAGAUUAUAACAUAGUGUGUGUUGACAGUGGGG
CAAGUAUACAGUCAAAAAUACAUAUACAAAUGCAAUGCAGGUACAAGGACUAUAAAUGCA
AUUAUCAAUAGUCAAACAGAAAAAAUUAAGACCUACAGCAGAUCUAGUUGAGAAACUAAA
AAAACAGAUGGAGGUAACCCAAAAGCUACUGAAACAAGAAAUCAGUACCAUGUCACGGAA
GAAAAUUAUUGCAAUGCAAACAAAAGAACAUAUUUUCCCCCAAAAGAAAGGUUCAGUAAC
AACUCCAUAAAAUUCUCCCGAGAAGUAACAGCAAACACUAAGUCCAUGAAUUCUAGAACU
GAGAAAGAAACUAGGUAAGAAAAGGUAACUCACAUUCAGUAAUGCCAAUCAG

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 [-494.42] kcal/mol.

2. The frequency of mfe structure in ensemble 2.83394e-31.

3. The ensemble diversity 520.09.

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