lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-655.40) is given below.

1. Sequence-
AUCCUGAUAAAAAUGUCAAGACAACUAGGAAAGGAGAAGGCACGAGAAAAUCAUAUUAAU
AGACUAAAAGAUUCAACCACCUUUGGUGACACAUAAUCAUCUAAAGUUAUACAUGAGAUC
CCAUUAGAUAAUUCAAUUGUAAGAGACUUCUACUUAGCAAUCAUAGGCAAAACCAUCUUC
UUAUGACAUAACCAACACAUUUAAGUCUCAAAACAUAUUUUCUAUAUUAGGCUCACAGGG
GCAGCCUUCAAGGGUAAGGCAACAAAGCGAAUGAUUAGCCAUUUUACUUAAUUUGAAGGC
AAAUAGAAUUAAGAGCCCUUUUGAAAGCUAAUUCUUCACUGUAAGAAUAAUCAAUAGAUU
UUACAUAAUCUUGGACAGAUAAGAACCAGAUUUCAGAUAUAAUAAUAUUUUUCCUGAAAA
AAGAAACAGAGUCCUUAAUCUUAAAAAGGAGGAGCAACUGAGGGGCAGGUCCUUAAGAUU
ACUUCCUGAUAAUUCUCUCGCGGUAUUAAGAACUAUGAAGACUUAUAGGAAAAGUGUGAA
GUGGAACAUAUCACAACUACAGCAGGCAGACAUGUAACAGUCUUAGAUAGCAGGACAUGU
AUAACAAAAUAUGACAAGCUUCCUCGAAAGAAGAAAACAGAAAAAAAAGAUUUGAUUAAA
AUGCAAUAUCCAAAACCUGUCAGGAUCAGUCCAUGGACUCCAUAAAAAUGAAAAGAACAA
GCAGUACACCAUACUUCAGGCAGACUUAGCACAUUUCACAAACACGUACUGAUCAGACUA
AACAGAAGGUUCUGACCCGCAACUGAUGAACUAGAACAGAGGUGAAGCCACAAGAAAACC
GUAAUUGUAAAAUAGGAAGUUUAGACUCUUUACAUAAUAGUCACUGCCUAUUUUAACCAA
UUUUAGGCACAUAAAUGACUAAGCAUAUAUACUAAAUCAGGUAGCUAUCAAGAAAACUCA
AAUGUAGCUUAACCAUUUCAAUAAUAUAAUACAGUCUAGUUGCGGCCAUUUGAUUUCAUC
AUCCUUCCACAACAUUCAAACAACAUAACUUUAUGCCAAUUUAAAGGAAAACAUGCUUUA
GUAACAGCACAUUGUUUCAAACUAAAACCUCUAUGUGUCUCAUAUUUACAGUUGCUCAAA
UAGAACAAAUAGAAUCAGGCCAUAUGGAAGGACUAUAUCAAAUAACAUUCAGUCAGUUUA
AGACUACUAGACAAAAUAUUUGUAAAGUCAUUGUUAGACAAAUAUACCAGGUUAAAAUAA
UAUCCACAUCCUCUAAGAGCAAAGGUGAAAUCGUACACUAGCUUGACCCAUUAUAGAUAA
AUUGAGUGAUUCAGAGGUUCAUGAGCCAAUUAAUAGACAGUUUUAAAUCAUGAAUAUAAA
UUAUUUCCAAAUCCAUAGAAUUACUGGUAAUUCAUGCCCAGGUUACCUUAGAAGAGAACA
AACUUCUCAACCUAAACUAUAAUGCAUAAUUAGGCAUCCAGUUAUCAAAUUAUUGAGAAG
ACAGGAGAAAAUCGGGUUCUUGUACAUAUCACCUAAUAUUCAGUGACUAUAAAGAGAAGA
GGACCUAAGCAGAAGAUAUUAACACCAAAACAAGGUCAGCUUAUGCUAUCACAUAUUCUU
AAAACAUCAGUCAACCUGCCAAACAAACCUUAACUGAAUCAUGAAUCACUAAACAACUCU
CCUUUUAGACACACAACUUAUCUUUGAAUCCCAACUUCAUUUUCUAUACAUCAUUCCCCU
AAAUGCAAUAUUCAAAGAGAGCAAGACAUGGCUUAAGAUAACUUCUGGCCAGAUAUACUC
CUCAAAGUAUUAUUUCGAAAGCCUUUAUAGCUUUAGGUGGCUCUUAAGCAGAUAAUAACC
AUCUCAAGACAAGUUCAAAACUGAUUCAAUAGCAGCAAACAUGAUUUACACAUUACAAAG
GUGAUCUUUUCAUUUUUCCUUUCAUCCUAGUCAACUAGGUUCUAUGCAUUAAGCAGAUUC
CAACAGCCACAAGCAGGUUCCCCUAUUCCGAGGUAUUAGAAACAUUCACACUAGUUAAAG
GCACAAAAGUUUCAGCAUUUCCCAGUUAAUUGGGACAUUAGGACAGGUUUGGACAUCAUA
AAAUAAGUUCCUAAAUUUGUAUAACAAGUUUUGGUCACUCAGAGAAGGCAUCAGUAUGCU
GAAGCAAGUUAUUGCUUUUAAGGAAAUUCUCAAGCAAUUGAAAUCAGUUCCCAAACACCC
CUUAGGACUAUAUAAACAUUUAAGACAUAUUUUGGAUAAUGCAAGACAGAUUUAUAAGGA
AAGAACCAGAAGCCAGACUUUAAUCAUGAUUUCGAGUCCUGCAAUUAAAUAUUUUACUUA
UAUCAAUCACCAGAAUUUUGAAAUAGUCUUGAAUUUAAUCUAAGUCUGCAAGACUAACAC
GAGUGCUAACAAGAAUUCAAACAGGAAAAAUGCGUCAAUCUGAGGCUUCUUAUUCAUAUC
ACUCAAACUUGCAACUGACUUAUAACCAUAGGCUCUUACAGCUACCAAUGAGGAAGACAG
AACUGGAUAAGAUAACAUGCAUCGCUUCUGAAACCCAAGACUUAUCACUUUGAUAAAAUU
UAAACUUGAGAUUCUUCCUAUCUAAAUGACAUAAAAGGACUUGAAGGAACCAAGGGUGUA
AUUAAACUAAGGCAAUCAGACACACGACAAAAAGAGAGAAUGUCACUGGUUUCUCCACUC
CUAAUGCUCAUUCAUUCCUAAUCAUGACUGGAAUGAAAAACCUAAAUGACUAAACUUUAC
AUGAUAACAGUCAGCUUCCCACAUCUUACUCUUUCUUUACUCAAUUAUUUCUUCUUUCUU
AAAUAAAACACAAGCAAAGAUGUCAUGAAAAGGUCAAAAUAGCAAGUAGCAGCACACAAA
AGGGUAGUAGUAUUAGUAAAGGGGCCACACAAGGCAACAAACAGCAUGUUAGUUAUAGAU
AUCAUAAGAUACAGAGUAUACUCAAAGUAAGCUAGCGCUUAGACAAUGAUCAUGCAUCAC
UAGUAUGUACAACAAGUGCAAUUAAAUAACAAAUUUAUCCAAGGCAAAAUAGUAAGAGAA
UGUUGUUAUCUGUCAUCUAAAUAUGCAACCUAUUAUCAAGAGCUUAGUCCGAACUAUUAA
GAGUAGAACUUAAGUCAAGUGAUACUCAUGAAUAUCAAAUGAUUAAAGACCUUUCAGGUA
UCUUUAUGACCUAAUAGAGAAAUAUGUUCCAACAGGGAGCCUUUAGAACCAGAUCAGGCU
CAUUAAAGCUCUACCUUGAAAACAUAUUUUACCUGAGAUGCAGGCAAACAAGCUCAACAC
ACAUUUCUUCAAAAAAGAGACUGAGUUCUAGCAGGCGCCUGAUUUGACGGUAUUUUACGU
CACAUGUGCACUUAAAAUCCUGAAGAGCAUGUUCUUGAGUAAUAACAGUGUGUUUUAAUG
UUUUUUGUUGAUUAUUUACAGGGUUAAGCCAAUAGGUGGAAGUAUGCAG

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 [-721.09] kcal/mol.

2. The frequency of mfe structure in ensemble 5.12259e-47.

3. The ensemble diversity 820.10.

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