lncRNA Structure Prediction

Species Name : Withania somnifera Sequence Id : GBHJ01008600.1

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-658.20) is given below.

1. Sequence-
AUACCUGGAGGACUAUGUCGGUCCGUCAGGUCGCAGGUAUUUAAAGGGCCUCUUAUUUUU
GUAAAUUUCAUUCUCUCCACUUGCCUCUCCUCUUUUCCUUAAUACUCAAGAACCCCAUUG
GUUGUGACUUUUCACUUGCCAGCCACACGUUCCAUCAUCCAUUUUUAUUGGUUUAACUUA
CAUCAUUGUGACUAUCUGGUCCUGAGUUACAUGGCUCUAAAUAAGGAUGUCUCCAACAGA
ACCCCUUGAUUUAAGGUAAAAAGUAUUGUGAUUCAAAAACCAAAUCCGGAACAAGAGAAG
AAAAAACAAAAGAGAUUCUAACCAACAAGAGGUAUCGAGAAAGAGUAAAUUGGUGGAUCA
ACCCACUUACUCUUUGAAUAGUGAGAAAUCUUCUAGUCCAUUGCCUGUCAGUUAGGCUAA
AUCUGAGGAAGAAGUUGUGGAUGAGGGUAGCAUUACUCCCGUGCGUUCACCUAUACUUUC
UGGUGAGGUUGAAUCCGAAAAGAGAAAGAGAGAGCAACUCAAAAGAAACAGUUUAGAGAU
CUAACAGAUUCAAAAUCCCAUGCCAACUAGCAAUCGUUGAAGAGAAGCGUUUGUCCAUUG
AGAGAUUGCAAGGUAAAUGUCCAUUUGUCCUUGAGGCCACCAAGUGACAUGGUUUUGAAA
AAUACACAAGUCCAUUGCCAAAGUUCAUUCCCACAUGGGUGUGGGAGUUCUAUCAGGCCU
AUAUAAAGGCACUCCUACCUAAGGCCAAGAAAGAUGACCCUCAAGUAUUGCCCGAUAGUG
UUCGUAUCUAGGGUAUGAUAUUCUUUACAAUUUGGAUACUAUAAAUGAGACCUUGGUAUG
AAUUACAGAGGGACAUACUUCAUGACGAAGAGGUUCAAUGUACAUCUUGAUAGUAUGCAU
GGUUGAUCAGCAUCUUAGUUGAGUGAAACAUUACCUCCCUGGCUUGCACUAGGUUCAGAU
AUAAAGAAGACUCACAUUCACAUCCCAACAAGGUAUUGGUUGAGCUUCAUCAGAGCCAGC
CUUAUGCCUAUUCAGCACAAAUCUGUUAUCCACCAUCACAUGACAGUGUUGCUUGGUGCU
AUUUUAUCCCAAGAGAUGAUAAAUGUUGCUAUGGUGAUUACACGAAGAUAGCUGCAAGAG
CUCAGAGUGAAAUAAAUUCAUAUGGUUUCCCCUGCUUGAUUAUUGAGUUGUGUCGAAGGG
CACUGGCACCCAGGAAGCCUGAGGUUUAUUUUGCGUUCAUGGAUAACUCCACUAUUGACU
UUUGGAGAUUUGAGGAAGAGUAUAGAGAUGACUAGGGUUUAAAACCAGCACUUGGUGAGG
AGGAGGCAGUACUUGGUGGGGGCGACCCAGAUAUUGAUCUUGAGAUGCUGGGUGGUGAGC
CCAAUACCGUUCAGGAGGAUGUCAUUCCUCUAUCUUCUACUACUCCACCUGCCAUUACAC
CUGAGGCUCCACCAGCCGAGACUUCAGUACUACCAUUUGUUAGUUCCAUUGGGAAACCUA
GGCCAUAACUAGUAUAGACACCACCACCAUCUACUACACCCAAAACUAGACCACCAGCAC
CAACAACUCCAGGUCCAGGUCAGGGUCUUCAUCUUACACAAGCAGCUAUCUAUAGGAUGG
UUCAGAUAGACUACUUAGCAGAGCAGAGGUCUAUCAGAGUAAAGACUCAGAUUGAGAGGU
UGGUUCAAGCUUCCAUGACACCCUUCCAAGAGAAAAUAAGAGGAUUCAGAUUAACUACUC
CGAGAUAUGGCACAUGGUUGGAUGAGUUUCUGUUCGUGAGGGUCAGGCAACAUAGUCAGG
UACAAUUUCUUGUGUCGACUGGCAGAAGAUGUAGGAUGACACUACAGUCUUUAGAGUGGG
UAUAGACCGAUUGACGACCCCUGACUUAGCUAGUAUAUUUGCAGACCCAUAAUCAAGGUC
AGGGAGUCCAUAGUGAGAAUCCACCAGCUCCAAAGACCAAGGGGGUUAUUAAUACCGGUG
UAGAGAAGACAGAUGUGUUUGGAGGCCUUUAGGAUUUGUAGGACCAAUUCUUGACUGGAG
GAUUGGAGAGGUCACUGGUUGAUACCCUACUGGAAGGAGGUAGUACAACGAUGGAUGUGA
UAGAGACAUUUUAUCAAUCCACCGCACCUACAUAUGAGAGGGUCACUGAUGUUUGCUCUC
GACCUUAGUCGUAUACUACUCAAGUGGCCCUUCUACACCCGUCUCUUUUUUUUCUUAGAC
UUAUAGCAUUGAGGACAAUGCGUACUUUGUAGAUGGAAGGGGGGAAUUGUUACUACUUUU
AUUUAUAUUUGGGUCUGUAUAAUUACAUUUACUCUCUUUUUCGUUAUCCCUCUCUCUAAU
UCUGAUAGUAAGAUGCUCUUUGAUGUGUAUAUGUAUUUUGGAUUUCUGCUUGAUAAAGUG
UGUGUUCUAG

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 [-697.30] kcal/mol.

2. The frequency of mfe structure in ensemble 2.79037e-28.

3. The ensemble diversity 559.33.

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