lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-636.60) is given below.

1. Sequence-
CUCACAUGUACCUUACUAACUUUUUUCUAUCACCUCCUCUCUCUCUCCUUUCUCUUUCCC
UCAAACCACAUCGAAGAAACUUCUGCAUCCCUCUAAUUCUGUCAAAACUUCAUCUGAUCU
CGGUUGAUUUCUCACCAACUACUUUAUAUCCUUGGUCUUUCAUCAUCAAAUGACAAAAUC
AAUAAUCUGUUUUUUGUUAGCUCUCUAUUUCUUCCCGUUAAUCAUACGAAAAUUAGUUGU
CAAGAUCUAGAUCCUCUUGGAAGAUUCUCAACGGUAAUUCUCACCUUUACCCUUGAUUUC
UCAUUGAUUUCCAAUUGUAUGUGUGUCUUUCCUAUACGAACUCAUACAACGCUGGUGCUC
UCUGAUUGGUUGUGUUUCAAACCUCCAAAUUUGAAUUCAAAUCUUUUCUUCUAAGCCAUU
UGACUUCAAAUUUCUUGGAGUAAUUGUGUGUUAUUUUGACACCUGUCCACUCUUAUCUCU
GUUUCCCCCUAAUUUCAUUGCCUUUGAAGCCCUGAUUUUUGGUUUUAAUAUAUACCCCUU
UUGGGUGAGGUUUUAUGGCGUCUUACAGUAUAGAGAGUAUCAGCCUAUAGUAUGAAAACU
CCCAAAAUACUAGGGUUUCUAGGGUUUGAGAGGAAUCCUCAGGCAGCUACACUAUGAAUA
CAAAUUUGGAAUAUUAAAAUCAUAUAUAAAAGGGGUGAAAUCAAGGCUCAAAGUAGUAAG
AAUCAUCAUAACUUGCUGAAAAUCCCAGCUCCUAUCAAAAAAUAGGUAAAAUACACAGAG
UCUCAUCCAUCUUUCUUCACCGUUUUUGGUAAAAUAAUAGGUUGUGAAACGUGUAUUUUC
CUAUUGUAAAGCGUAGAAGUGGCUUUGUUUGGAUGAAAUAUGCAAUCUUCUUUCUUAAUU
CUCUUACUAUUUGGAGGAGAAUAUAUGGUUAAGAAUAUGUUUUGGUUGCUUUCAAGGCUU
UAUAUAUGACAUGUGUUACUAUAAUAGGGUCAUUUAGGUGUAAUUGUUUUGUUAUUCCCU
UUUGCUAUCUAUGCCUUGUUGUUAAAAGCAUGUAAACCCUACCCUUUUCUUUUAUGGUGC
AAGCUGCCUUGCUAAUAUAUAUAGGGUCUCCUGGUCAUGGUUUACUAGUUGAUCACUUAC
CUUGGAUUCUAGUUAAAAUGAAUAUUAGUCCAAUAAAAACAGUUAGUGUUAAGUCUAUGC
UAUGUGUUUCUUUGUUGUCAUUAUGCAUCUGGUACAAGUUUAUGACUUUGAUUAGAUUUU
GCCAAUGUGUUGACCUAUGAAGCUGCUUUACUUGGUUUAUUUGGCACGAUAUCUUUCAUA
AAUGUCUUUUGUUUAAGAAGUAGGCAAUGUCUCAUCUUCUUUUGAGUGUUAAACUAUUUA
AUAAUCUGUGUAGGACUUGACUGCCUAAAUGCCCCUGUUUUAUGUUAAAGAUUGAAGUUU
UAUGGCCAAAGUUAUGUGAUGUGUUGUCAAUUUGAAAGCUAAAUUAUCUAAGUGCAAAAU
CAGCAUAUGUAAUGUUCUUCUCAAGGUUUAUUUGAUUUUUUCUUUUCUCUAUUUCGUGUC
UAUAUUUGGAAUCUGUGAGUCCAUUUGAAUGGCAUCUACCGUUACUUGCCUUUUUUCAUA
UGGUUUUAGCAGUAAAGAUGGGAUCUUUAAGGUCCUUUUAGCAUAGUAUCUUAUCUGUUG
AGCCUACCUGUAUUCAAGAAACCUCUUGCUUUUCUCUAAAACUGUCAUUUCUUCUACUGA
AACCAGUUCCCUGGGUGUUGACGUUUGGUCUGUCAACUCUUAAAUGUUGUAGGGUGUUAG
ACAUGCCUAGGUUUUUUAAGUGAAGUUUGUUGACAUGUGUGUUGGCUAUUUGUUUAUUGA
GUUUCAUGGUUAGCUGUUGGUCCUUUCAUUGCCUUAACAUCAUAAAUGGAUGAUAAAAAA
GUACUUUUCUUUUUUGCAUAUGUUUAAGUUGAGAAUGAUUAGAUGAUAUUGAGAAACUGA
UUUGUAUUUGAAGUUGUUUGUUUGAAGUCUUAAUAAAUAUGUGUGUUCUAAUGAAGAUAU
AUGAUUUCAAUGUUUGGAAAUCAGUUUGUAGUAACCUAUUAAGGUUAAAUACUCUCAUGC
UUGCAUCACUUUCUAUUAAAGUUCAAGUCUUCUGGUCCAUACUACUCAAGUUUUGAUGUG
UAGUUAACUUAUUUUCCAUCUCAUCUAACCUGUUAAAACAAGGUAACAAAAAGAGUCUGC
ACAUGACCGAGUGAAGCAUGUCAUCUUUGUUUAUUUUAUGUGAUAAUAUGAAUUGAAGUG
UGGAAUUUUCCUUUCUUUUCCGUGGAUUUGUCACAUGCCUAGGUUUAGGUUCAAUAAUCC
AUUAUUGGAAUCUGAAGAAUGAAAUACAAAUUUUUACUUCUUUGCUUUCUUGCCGCUGGA
AAAUCUGUUAAUGUGUGUAGAAAUCAUUUAAGUUCUUCAUGUUCAAUUUUCUUGAUUUUA
UUGAUUGAUUGUUUAACUGAUUCAAUUAAGUGUUGCUUCAAAUACUCAUUCUGCUUCUCU
UUUCUUUUGCAUGACUCCCUCUUCCGAGUCCAUUUUGGACUCCUUUUUGCUUUAUCGAGU
CAAACACCUUGCCAAGCCUUCUUUGGGCUGAAGAAAGAAAACAGGAAUUGGGCCUUAGGC
CCUUUGUGAGACGCAGCAGUAGUAGAGAAGUAGAAGAUGGUCAAACCUAUGUAACCUGAA
GUCCAUUAAGAUAGACAUUAAGUAUCUGUUCUCUUAACUUAUUUUCUGCUCAAAUAAAAU
CAGAUCAGAUUCAAUAAAAUCAGAUCAGAUUUUAUCCAGCAAAAUUAAUUUAAUUCAGUU
AAGUUUGUUAUUAUUAUUAUUAUUGUUAGUAAUUAAUUAAUUAUUAUU

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 [-688.17] kcal/mol.

2. The frequency of mfe structure in ensemble 4.60364e-37.

3. The ensemble diversity 761.78.

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