lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-789.40) is given below.

1. Sequence-
GGGAAAUUUGUUUUAGAUUAAAUUUAAUACGGAAUAAUACAAACUAAUAAACACAUUAUA
CCGAAGGAAAUAUAGGGAUAAGGUUUGAGGAUUUGGCCUUGGGCCCAAUUUAGUCUCCUU
UCUUCUUCGGCUUCUAAUCUUCAAUCUUCAGUCCGUUUCGGACCUUGGUUGAGAUUGACU
CGAAGACUUGGAGGUUUUUAGCUCACAGAAAUGCAGGGAUGAGUACAAAUAGAACUCGAG
AGAAGUUCAUGCAAGAAAAAGGAAGAAAAGAAUUAGUUUAUCAUCUUAGAGUAAACACCG
AACUAAUAAUUUCAAACCAAUUACAACUCACAUACAAAACUCAAACAAGCAUAGUAGAAA
CAUAAACAAUUUUUGGGCCUAAAAGUCCAAAAAAAAAAAAAAACAGUUUUAGGACUAAAU
AACGAGAACAAAAAUCUUUAAGAGAUCUUCAACAAGCCUCAUAAAAAUCAAGAAUCUAAU
UGAAACUUAAAGGAGCCAAACAAAUGCCUCCUUAUCAUAUUUAGACAAAUUACAAGUAAC
CAAACAAAAUCGUGAUUAAGACUGCCCCUUCACAAGUCCAAAGAAUGCUUGAGAAAACAA
AAUUUGACUGCAACUUAGAUGAACAAAUAGACUCGUAUACCAAUGAGUCAUCACUUGCUG
AGCUAAUUCAAGUACAAAAGAAACUGGAUUGUUUGUGUAGAAAUAUUUUGGGAGAAAAAG
GGAAGACAAGGGAUGAUGUAUAAUACAAACCAUUCAUUUUCUCUUCCUAAUAUAAUCAUG
AGAGCAUCCCUCUUCUCUAAUUCCUUAACAAUUUAAACCAACAAGCUCUAUUUGUAAGCU
UAUCAUAUAGGAGCCGAGAAGCCAAGUGAGCAGAUUCAUUAGCGAAGUGAUAAGUAUAAG
AAAGGUCAUAUUUUUGCUAGUGUUAAUGAUAUACCAGUGACAUACCGGAUGAAGAUGCAG
CAAACGUACACUAUGAGGUAUAAUAAAUCAUGAAAUUCCCCGCUUGGAUGUUAGCACAGG
GUUACCCAAAUUAUCUGUAUAAUAGUUCAAACUAGAAAAAGGAAAGUGCAGGAUUGAUCU
UUUGCAAAAGCUAUACUAUCAGCCUUAUUUACAAGAAAAGGCAGACAAGAAUAACAAAAA
GCUGCUCACGCUGUAUAAUCCGGGUUAACAAAAUUCCAGCCCUGCUUCAUUAUGAGUAAC
ACCUUUAUCAUGCAAUUAUUAACCAAAGAAACCAUAUUUUCAAAGCAAAUAUCAGAAAAA
UACUCUAAUCAGUUUUUAUGACCAAAGAAGACCUUCUCAACUAGAAUGGGAUUGCAAUGC
AUAAACGUAACUUAACAAAGGAGAUCUGAAUGCAAGUAGACAAGCUGACAGAAGUUAUUU
AAUCCAACAUCUCAGCAGGGAUGACUAAACAGAACCAACUAAAAACAGAACAAUCCAUUC
AUGAUUAGAGACAACAUUUUCACUCUAAAAUGCUUAAGGUGAGCACUAACUAAGACAUGU
UUUCACGCAGGAUGAUGCAAUAUUUACAUGUAUCACAUAAUUCUCAAUAUUAUUUAGAAA
UAAUAUCAACAAAUUAACGACCAUUUACUCUAUCUAAGAAGAGCAAGUGUUAAUUGGAAG
CCAAACAGGAAAGACCGUAACUAGUUGAAAAAUAGUUUUCUCAAUAUUAAAAGAAAAUAA
AAUUGAUCAUGUUGGCGCACACACGUAGUGAGUAAAGAAAUUUUCAUGGACUGUGUCACA
AGUGCAAGUUUACAAUACAUGGCCAACAAGUAAUUGGUAAGGAUCAGUUCUAGAACAGAA
UAGGAAACAAAUGUACUAAACAACAGGUUAUUAGAUUCGUCAAAAUAACUUGCGAAUUUC
AAAAGAUAUAUUAGAACAAGGGCAAGGCCACAGAAAAAGUUUAAUUAUAAAAUUUAGGAU
UUAGAUACAUACUCUCACUGCUUAUUUGUAUAACAAAUUUAAGUAUAAAACGAUCACACA
UUCACAUUACAUUAGAGUGCAAGCAAAAUUAUAAUAAAAGAUGACUAAACCAUUUCCCUG
UUGUAAACAAACUAAGCUUUAUAACCAAAACCAACAAGCUCAAACAAUUUGCAACAUGUU
CAGGUAGCAGGCCUGGAAGCAAAUUUCAAAACUUACAGCCUUAAAUUAGUCGUCGUGAAA
ACAUGUCAUACAAGUCUAAAGGAAAUCAGUCAGCAAACAACUUUAGUUUGACAUACUUCU
AAGACUUAAAUCUCUAGGAGAUUCCAUCAUAAUUGAUCAUAAAAAUAAAUUAUUUAAAAU
AGGUCAUAUGUAUACAGGCCACAAAAAUAAACCGCAGACAGAUACUGUUCAAAACUGGUU
GAUUUGCAAGCCAUGAUCACAUAUGCAUUAAGUAAAUUUUAACCUACGUCAAGCUUUUUA
AUUUAUGUAAAACCGAAGAGACACUUCCAGAUCUCAUGAGACAAGUUGAACAUAUUCUAA
AUACUUAUAAGACAACUACAUAGACCAAAUUCAAAUAUAAGCAUAUUGCCCAAAAUUAAA
AAUAUAUCACACUGGUCAAUUAGAAAACAUUGUCCUUUAAUGAAAGUCAAUAAAGAAAAC
AAUCAGUUUCCAACCAACGCAGGAAUGAAGAGACUUGGACUUUUAUGCACAAAGACCCUA
CUCAUUGAUCAACCAAGCACCACUAAACAUGAGGCAAGUUACUCAGCCAUUCUCAGACAG
CCUAGGUAUUUAGACAAGUUUAACACACUCAAAACAAAGCAUUUAAACAGAUUACAAAUA
UUCUUUAUAGAUUUCUAAACAUCACAAAGCAGGUUUUAAUUUUUUACAAUGGGUUCCAUU
ACUUAAAAACAGGUUCUAUAUAUUAAGACAAUUUUUAACAGUUAUAGCCAGAUUUUUAAC
CAAUGCAAGUCCCUUGACUUAACUUUCAGUUAUUCCAGCCAGAUUAAAGUACUUAAUCAU
GAUUUUAUGAGCAAUUUAUAAUCAUUUAGUCAUGUUACCAUUUUUAAGGUGACAUUGUGC
AAUGGGUGGUCGACAUGUUUUCAGAAUCAAGCAAACUCAUAUUAACAUACUUUUCCUGAG
AAACAGCUGAAGGAGGAAACAAAGGAACAAAGCUAGCUUAGCAUGGAAUUCCAUCACAGG
AGCAAGCUUAAGAUAACAACACUUACCAAGAUUCAGCAAAUCAACCUUGUACCUGAAAAC
AACAUGACUAAAAUGGUUUAUAAUUGAGCUUACUCUUAUGUACUGAUUUUAACCUUAAAC
UACAUGUUUUCCUUUUCAAUGCACUUAUUAAGUUUCUACACAACAAAUAACACAUAGAAG
UCUCAAAAUUAAUCUAAACAGUAAGUAAAGAUGAGCGUUUUACCUUUUUAACGGCAGCAA
ACUGUGACUAACGAACCGAGGGGAUUCCACUAAUUGCGAAUUAAUUAUAACUAGAUUAGA
ACCUCUCCAAUCUCUAAUCCCCCAUAUAGAUGCAAGAAAAGCCCCUUUAAAGAAAGGUCG
UAGGGGUUUCAGAUCACCUUAAUUUUACCUCGUCGAUCAAAAAAAAUAUAAUUAAGAACC
UUAAUCCGCAAACUAGGCUAGAACCUUAAAAAAAAUUGGAAUCCGUAAUACCUAAACCCU
AGCCGCCUUAAAAAACCCCUAUUUCUCUUCCUCUCAAGCAUGAGCUGCCCUUAGCUCUAU
UACUACCAGCUCUGCCCUUCACAAUUAAGAGGUGAGGGUUAUUUAUAGAAUAAAUUGGGG
CAUGAAAAGAGAGAGAAAACUUGAGGAUUUGAAAUUCAAAAGGGAGUCCACUAUCCAAUC
AAAAUUAUCCAGGAGCUAUGUACGAAUUUUAAAGGAAAUGCAAGAAAUUGAAGGGGAAAU
CGAAUGUCACCGUUGGAGUGACACCUGUACAACUUCUAGAACAUGGACAGCUUGAAGUUG
ACGGAAUUUGGAACUGUUACAGAGGCUUGAAGUUUGGACGUCAUUUGGAGAUUGUACCUG
AGGUCAGUUUGUCGUUGUUUGACGGAGCUUGAAGCUCGUCUGUGAGGAAGAAACUUCGAG
GAAAGAGGGAAAGGGAAAGCGCAUAGCUUGAAAGGUUG

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 [-861.30] kcal/mol.

2. The frequency of mfe structure in ensemble 2.15445e-51.

3. The ensemble diversity 1094.92.

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