lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-556.50) is given below.

1. Sequence-
AUGAACUAAAGAAAGUAACAAGUACCAAAUUCAAAUUAAUUUAGGUAAUUAAUCUUAGUU
UAUUUCCAAUACUGUCUCUCUCAAAACCCAGAUCUUCAAAUUUGAGCCUGUUAUACAUAA
UAUAAGGUUUUGUAGAAAUCAAGUACCUUAAUUAGACUCUCCACUAAUUUCCUAAAAUAU
GUAGCAUCAACAAAGUCAUCACUUCAUGCUUAGACAAUUUUAGUUUCUCAUCAAUUGGGG
UCAAGUUAAAUCUCUUCAAAAUAUCAUCGACAUACUUUUGUUUCUGCUUGAUAUCAUUUA
ACUAGGUUUGCCUUAAAGUAAUCUUCUUUGUACAGUGGAUUUGUAUUUGGUCGUGUACAU
UUGUUUGAAUCCUUUUGCCUUUCUCUAGGUGGUACAGUUGUAUCACUAGCAAACAAUUUG
UUGUUCUCUCAACACAUAAAUUCUUGGGCAGAGGCUCGAAAUUGAUUGCAUUUUCAAUAU
CCAUAAUUAUGUACUUGUAUGAUGAUUCUGGACCUUGAUCAACCAUUUCUGCCAUAAAAC
AUGAAAAACUUUUUCUUGAUGAAUCCAACUUCUUUCAUUACCAGUCCAUCUUGACCUUCA
AACAUUUCUUUCUAGUAAAACACCAACCUCUUUCAAAAAGGCACAAUUCUUUACCAAAUC
AUUCAUUCUAGUCAUCCGAUGAAUAAUUGGCAAAACCAAUGCGUCAUUUUUCUGUUGAUU
UAAGAACAUCUCAUGUGUCACCAAUUCACCUUCUGGAUCAUCUAGUCCCAAGGUGUUAAG
AACCUUGGUAGUCUUAGAGCCUGUUUGGAUGGUCUUAUAGCUUAUGACUUAGAAGCAUAC
UGAUGGAAAUUUACCAACACAAUACAAAUUCCCCACUUGCAAGAGUAAGAGGAUCAAAAA
CAGCAAAUAAAACAGUAGUUACAAGAAACAAAGGCACCAGAUUUUACGUGGAAAUCCCUU
CAAAAAAUAGAGAGUAAAAACCACGGGUCACAAGAACCAUCAAACAAGCUCCACUAUGAU
CAAAAUCAGGUUACAAGAGAGAGUCAAACAAGGGCUGAAAUAGUACAAUAAUACUGCAAA
UAGCUUCUCUCCAACAACCACAACAAAGAAGCAAGCAACUAGAGAAAACGCAGAAAAUUU
CAGAAAACAGGACCUCUGUUCAUACACGAAUAUCUCUGCCUACAGAUCUCCAAAUCAAAA
ACUGACCAGUAGAAAUCAAGUUCAAUGUGUCCCGAACCUGCCUGCAAAAUUUCAGAACAA
UUGGGCACUGUUUGACCCUCCAAACACCAGCUCGAAAUAUACUGCAAGCAGAAAUCCGAA
AGUGAACAGCACCUUCUUCCUCUCACGAUUUUCUGGCUCACACGCUCUAUUUUUCCUCCC
AGUUUUUCGGCUGCUGUAAACUCCUAAUUUUAUCAAAACAUGAGCUUGUAAUAGUGGGCU
UUAUUUGGGCCUCCACAUAGGAAGUGAGCCCAAACCCAACACAUACUUAUGGCUUUUGGC
UUAUUUUUGUUAUUUUGACUUAAAAACAAGUGUUUAAAAGCACUUUUUCAAAAGAUUUAC
UCACACUACAAAAAAGUGUUUAAAUUCAAUCUUGGCUUUAAAACACCUAAAAUAAGCCAA
UCUAAACAUGCUCUUAAGCAUUGUCUUCUUGGUGUGGAACUUCAUACUUAGAGAGUGCAA
UAUCCUUUCGACAACUUUGACUUCUUUCAAUACUUUUCGGAUCCCAAAAAGUUUGAAGGA
UUCAAAAUUUCUUAUAGGAUAUCACAGAGACCAUGAAACUAAUUUGAAAGAUCUGAUAUG
GAGUUAAAAGUUUGUGACUAUCUCGUCAAAAAGCUUAAGCUAUUAGGGAGAGUUCACAUU
UACUUUUUUAAUUAUGUAUCCGACAUACUAAAUCAUCUUACUUUACGAAACCAAUCGCCC
UAUCACAUUUCAAGUGUGCCAGUUCUAUAUAGAAGUUAUCCCUAAACUAAACUGUCUGAA
CAACUUCAAACUUCAAUUUUGGCUCACUUUUUCAAGUUGGUCUUGUUUAUACUUCUUUUC
CAUUCUUUAGCGAGUACAUUACAUUGUGAUGAGACGACAGAAGUAGAUGAUAAGAUUGGU
UUCCAUCAUAGAGACCAUUCCUUAAAAGAAUUUCUUGAUGCAGGUUAUAGAGUGCAACAC
AGUACAUUGACCUUGGACAAAGCUAAGAUCCAGAGAAGAAUAUUGACACAAAGAUUCUAG
UGACUAUUCGAUAUAAUGUGGAUGUGUGACAGAUUAUGGUAUCAUACUUAAGCCUUAUGC
UGUCUUUGCAAGAAUAGUCAGUGUGUUGUUGGACCAAAUAAAGGAAGAAAGAAGGGAGUG
AGUGUGUGGGCAAGAAUUAAAACUUCAGGCCCAAGGCUUCUCAUAGUUUUGAGUAAGCUG
GAACUCUUAUUUUAUGUCUCUUGAGCUUCUUUUUUAGUCUACUACCACCUUGUAUUCUUG
UAUAAGGAAAGAGGAAGGAUUAUAUACUUUAUUUUCUUGUCUAAUUUGUUAUGCGAACUA
UCCAGAAUUCAUUUUGCAACUAUUGUAUAAAUGUAUCCCUUAUUGCCUUCUCAAAAAAAA

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 [-602.96] kcal/mol.

2. The frequency of mfe structure in ensemble 1.82656e-33.

3. The ensemble diversity 773.96.

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