lncRNA Structure Prediction
Species Name : Withania somnifera Sequence Id : GBHJ01014495.1
I. Result for minimum free energy prediction
The optimal secondary structure in dot-bracket notation with a minimum free energy of (-320.20) is given below.
1. Sequence-
GAAGGUGGGAAACAGGGAGAUAAUGCAAGCAGUUCUAGCAGCUCAAGCAGUUCUAGCAGU
GAUUCAGGAUCGUCUCCUAGUGAUUCUGAUAGCGACAGUACCUCUUCAUGUGGAUCGGAU
GCAGGACGUUGACCUAGGAUGGUAAAAGAUAUUUGACGCAAGUGGAUGAAAAUCUUUUCA
GAUGUUUUGAUUCAGAACCUCAAGUUUGACUCAUGUGGUGUGGUUCCUUGAUGAUACUUG
GAGGGCAUAAACAAAUAUUUCAUUUUUACAAUCAUUUAGUUAGUGGGUCUAUUCCUAUAC
AAGGUGGUCUCUGUUAUGGGACUGAAUUCUAAAACUGAUUGGUUACAUUGGUAACGGGGG
GCAAGUAUAGCACCUGUAAAAUAGCCAAGUUGCUUGACCAGUUUGCUCAAAAAAAAUCUU
GUGCUGGGAUUUUAUUCAUUUCAUUGCAGUGUUGUAAGAGCUGUAGGCAUGAUUGUGAGG
UCAUGCAACUUCCUGGAUGUACAAUUAUGUACAAUUUCAAGUGCAGCUUAUCACAGGAUA
ACAUGUCUUGUCACUGUGUUGUGUAGUUUAAACCGUGAAGUGAAAUUGACCUUAGACUGU
GUACAUAUGUAACUGUUCUUUUGUUUUAUUGGGCAUGAUUCUUGGUAAAGAGGUUGUAAC
AGUUACUUGAGUAGGUAGAUCAGGGUUGUUGAUAAAAUAAUUUCUUUGUUAGGGGUUAUU
UGGGCUCUCAAAGGUCCUUACCCCUUUGCAUGUCAUGUAGUGUCUUGGUGGAGAUUUUGC
AUGUAUAGUCUCUCAGAAAUAUAUAUAAUUGCUGCAUGGUCAACAAGGUGUUAAUCUUCC
AUUUCAACUAGUAAUUGCUGGAUAAAGAAGGACCAGACUGCAGAUUACUGAUCUCAAGAG
UAGAUGCUAAGAGCUGUACUUCCGUUCAUAGACUAGAAAUUACUCACACAAGGUCACACU
CCCAAGAGAGGAAGUCUCAACCAUCUGGGGUCUCAAUAAUCCAAAGAAAUAGAGAUAUCG
ACGAGGAUGUUAUGCAUUGUAUUAGUGGGGUGGAUAAAAGGUUUGUAUUUUGAUGUUUUA
UGUGAUAAAAGAGUGUGUUACCAAGCCUUAGGUUAGUCAAUACAGCUAUAUUGUAUGAGU
CAAAAGUUUAUGUACAGUUCGGAUGUGUAAGAGAAGAUGAUGAAGAAGAAGCCUAUACAU
AUUUUGUACUAUACAACUGACUCUGUCUGAGCGGAAAUCUUUUGAUCUGUUAGUGAAAAC
CUAUUAAAAA
2. MFE structure-
..((((....(((((((((((.......((((((((((((((((.(((((((((.(((((...(((((((((.((...)))))))))))...((((.((.(((...(((.((...)).))).)))))))))(((......)))..(((((((((((.......((((....))))..)))))))))))((((....((((
...(((.(((.((((((((((.(((....))).))))).....((((.......(((((((.....(((((.((((((((.(((((((....(((((((((((((((((((......)))))).............(((((((((....((((((..((......(((((...)))))......))..))))))))))))
)))............)))))))).)))))....)))))))..)))).)))))))))(((((((((.((((((((....)))))))).(((((.(((.((((((....)))))).....((.((((......((((((((((......))))).)))))...)))).))....))).)))))((((((((((((.((((((
.(((.((.(((((((((......((((((((((.......)))))))))).......))))))))).)).))).)))).))))))))...........))))))..(((.((((((.....(((((......)))))..))))))..)))...(((((((.(((((....))))).)))))))))))).))))..)))))
)).......))))))))))))))).))))...)))).(((.(((...(((((....)))))....))).)))....))))))))..))))..))...))))...)))).))))))))..(((((((((..(((........(((.((..((((((((((((....((((.....)))).....(((.((((.......))
))..)))....((((((((((((((....((((.((((.((....)).)))).))))....)))))....)))))))))...........))))))).......)))))..)).)))..((((((.....))))))((((((...((.((.((((((....((((((((..((...................)).)))))
))))))))))).))...)))))).)))))))))))))))))....)))))).......))))........
You can download the minimum free energy (MFE) structure in
II. Results for thermodynamic ensemble prediction
1. The free energy of the thermodynamic ensemble is [-341.68] kcal/mol.
2. The frequency of mfe structure in ensemble 7.37023e-16.
3. The ensemble diversity 328.13.
4. You may look at the dot plot containing the base pair probabilities [below]
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).
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.
