lncRNA Structure Prediction

Species Name : Withania somnifera Sequence Id : GBHJ01023312.1

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-426.40) is given below.

1. Sequence-
GGUAGUUGUUUUUUCUGCUAUUUCUGUGUCAAUUCUUACAUAGAAUUUACAGCAUAGUAA
GAAAUAUAAGAUUCUAUUUUUGUGUGAAUUUCCAAGUUCACUGUUAAAGAGUGUUUUUCC
UCAAUGAGAUGAAGGGACAAGGGGCUUUUUCCUACACACACACACACACAAAGAACGUAC
UUUUAGUUCCCAGUUCUUCAUCCUUAAGCUAUUAUUCAAGCAUGAUUUUGCUUUUCUAUU
GGAUUUGCAUUUUAUUUUCCUUCAAAAGCUAAAUGCAGACUAUUCUUGCUUCUGUAAAUU
GAAAUGCAGGUCAAAGUUCUAUCUGUUUACUCUCUGCAAUUUGAUUCUGAGGUAUAAUGG
UGAGCUGUUGAAUAUAAGUUCUGUAGGAAAGGUAAAUACUGGUAGAAAAAGGUUACUUUA
GUUAUUCCUCCGAAUCUAUGUAUGAUUUUGUGAAUUAAUUGUUAAAGUUUUGUGAAUUGA
GGAAUGGUCCAAGAGAGCUUCCUUCAGCCCACUCAUGGAGGAGAACUGGGGUUGAAUUAG
CUGCCGACUCAUUCAUCCAACCACUCAGUAGAAAGGAUAGGUUUUGUGCUGCUGUGAUUG
AGUGAAUGAUGCGGGAGAUAGUUUUUUAUCCCUCUCUUUCCUUGCUUGGACUGAAGGGAG
CUCCUUUUUCCCAUUCACUUCAUUUACGAAACACUGAAAACCUAAUUCUCAAAAACCUAC
CUCAUCCCUGUGACUAUUCUGUUUAACAUAUUGAGGGGAUUUCCAGGAUAAGAUCCUUUA
GUUGUCUGGACAAAUUCAAGCACUGGAUUACUUCUGUUAAAAUUUGUCAAUGGUUUUCUC
UAGCUUCAUGUUAGUAAUAUACGUCUAUGCACUAAAAAUCUACUUCAUCAUAUAAUUCCA
AGAGUUGUAUAUAGCCAUUUAACUAGGCAGUUGUCUCCUGUUGCUACCUGCUGGUCUUCA
CACACCAUUGUAUACUAUGGUUAUAUUUUCAUCUCUUAUACAGUUAGACAACACAGUGAA
AUGGUUGUAUAAGACAUGAAAUGGAUUAUUUUGUCACCUGUCUGAAGAUAUCUAUUUAAA
UUUCGGGAGAUAUUCAGUAGAAGUUAUACUGUGUAUCUAUAUUGUUAUAUCUGCUCCUUG
CAAUAUGUUUUAUGUGUUGAUCAGGAAGGCAAUACAGAUGCACCUACUUUAACUGCUGUA
GGAAGCUCUUUUUCCUCUACAGAGAUGUUUGAAGUCGCCACAUAUUUCUUGCACAAAUUA
AGGUUUCACUUUGUAGAUAGAUUCUUUACACGUCUCUUGCAAACUGAAACAACUUGAAUA
UAUGUUUUGGAGAGUAGGCAUAUAAAAAAUGAAUGAACAUUUGUAAAUGCUUAUUACCCA
AAACAGAAAGUAUGAAACUCACAUGUAUAUGAGUUCAAAUUGAGGUGGAAGUGUUUCUUG
GCUUUAAUAUUUUCAAAUAUAUUUGCAUGGCUUUCUCAGAGAGACUGAAGACUGCGAAUC
GUGAUGAGCCCCAGUUUUUUCUCCCUGUUUCUAGGGCAAGCUUGUAAUGAGGAUGACCUC
AUUGAAAUGCAUUGGCUCAAUUUUUAUAUGGCAAGUAGUUUGUGG

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 [-454.84] kcal/mol.

2. The frequency of mfe structure in ensemble 9.06267e-21.

3. The ensemble diversity 448.16.

4. You may look at the dot plot containing the base pair probabilities [below]



Download Dot plot

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

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

* Results have been computed using RNAfold ViennaRNA-2.5.0.
* An equivalent command line call would have been RNAfold -p -d2 --noLP < test_sequenc.fa > test_sequenc.out
* A dot plot into the mountain plot coordinates transform using mountain.pl test_sequenc.fa | xmgrace -pipe