lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-659.39) is given below.

1. Sequence-
AUAUGCAUGACAACUAAAAAAAAACAAAAAGAAUAUGAUCCAUCUAACCUCUAAGUGUCA
UAGAACCCCGUUAUUAUUGGCAGUCCGCUUUGGUUUAGCACAAAGAUAAAUGGUUGGAUA
ACAAUUUGUCUUGCUUUUUGGAGUUCAACACUCUCAAAACAUCAAUGAUUUGGAAGAAGG
UAUACUAUAGGUCCUGCAAACGGAUUGAAUAUGACAACCCAUUAGCGCACAAACUAUAAC
AGUCUACCAGCAAACUGUCUUUUUGCGUUCUACUUUAUGAUUCUUUUUACCAUAGAAGUG
GAAUAAGUAAGAGAACUGAUCAUCAGAAGCUUCUCAAUGCGACUGCUGCACCGAGCUGAA
CUUUGAUACUUUAUUCUUAAUUAUUACUCAAGGCGUAUAAUAAUUUAACUUUAAACUAUU
ACAAAUUUCUUCUGUCAAUGCCUUUUGUGCAAGGUUGUCCUACCUGGAGCAUUUCAACAU
CAACCAGACCUUGAUCUUCGCCAAAUUUGCAACCCACGCCAUAACACCUCAGCAAUAGAG
CUAUCACUACGCUCCACACCACACCUCAGCAAUAAAGUAGAGUAACCAAGAAACAAGGAA
AAGAAUUUUGUCAAGAAGAAUACAAUUCCACAUCAGGGUGGGCAGCGGAGGAAUCAAGCG
GACUAAAAAUACACUUGCUAUGGCUAAAACUUACAAUCAGAAAACAUGAACGACUAGCUU
GGCACUUUGAUGACAACUAUUUUCGGUGGGUGCAGAAAUAGACAAUUAAGUUCAAAAAGU
UGAAUCGUCUGUUAACUUCAACUCAUAUUCAGAUCCAAAUUUGGAAAAAUACUUACCCAU
AAUCCUUGUUUUUAUUGUUUAUUAAUGUUCCAUGACCCUUCUGAGGCUUAAUUAAAUCAG
AUACAGUUCCAGUAACUAUGUUCAACCACCAACGAAAGAUGAAACUAAGAACUUGUUCGA
AGAGUUUUGAAAUCACAACUAACCAAUUUUAUGGCUCAUGCCAACCAGGAUACAUCACAA
ACAACAGCAGGAACAGAUAUCAAUCUAAUUUAAAGCAAUCCCUUUCUUACUGCGCAUACA
GGAAUUUAAGGCAUGGCCACUUCAGAUUCAUCAGUAGACAUCAAAUACAGAUACAGCCAA
AUCUAUGAACACGAAUCACCAGUAAGCUGAAACAGAUCCAAUACACUUCAGAAACGUUGU
AAAAAAAACAAAAACGACAAACACACAUGUCAAACAGAUCACUGCACCAAAUAGUGGUCU
UUAGGAGCAUGCACAGAGCUAGAAACAAACAUCAUAUCAGGUUCAAAAUACAAAUCUACA
AAUCCUGGAAACAGAACAGUGACUUAAACAUGAUUGUGCUAAAAGAAACCACCCUCCCCC
GCACAUUUUCAUCAUGUGUUGGUUGACCCAACUGGCUUCAUACCGUCACGCCUCCCCCAG
UCCGCCCACAAAAGAAAACAAAGAUAUUAGGAGAUGUCUGCCUUUUCAUCAAACGAAAUU
GGAGAAAUACCAACAGGUUCUUCACACCAAAAAGGCUAGGAGAAUAUUGAUAAUUCCAAU
AAUCACCAAAACAUGGACUUCUUUGGGAAAAUGUUCCAAUAAUUCCAAAAAGAUGACUUU
AUAGGAAAAGCUAACUAAGAAUGCUCAUUUUCUUUUUUUCUGCUUUUAAGAAGUGAUAGA
AACACCACUGGUUAUUGAGACAAAUAGAAAAUGCACACAACAUAGAUUUUGCUUCUUGCU
ACAACGUGGUAUUUGCGAGUUUCCAGCCUUCCCAACAGCACUCUAGAUAUUACUUAAUUA
ACUGUGUAUAUAGAAAAUUCUAAGGAAUCAAUACAUAUAUAUGACUGUCAGAUUAUUUGA
UUAAAAUCAAUGACCAACAGAGCAAAAACAAUAACCCCCCUUUUCACCAGCUAUUGAAAU
AAAUAGAAAAUGCGAGCAAACAUUGUACAAUUUGGAUCCUACCACACAUUUGUAUUUUUC
CCAUCUUCACAUAAACACUCUCAGAUAAUUCUAAUAAAAAUAAUAUACAGAGAUUUUGUC
UGCAUCAAAUAAUUUGAUUAGGAUCAACAAUAUCUGACAACAUCAUAAUGACUGAAAAUA
ACAUGACAGAUGAUCUAGAAGGUCACAUUUGCCAGAUCUUCAGCAAGAUUGCCAGACAGG
AUACAUACAAGAAACAGGAAGUACGGGUAAUUUGUUAACAAAACUGACAUCAAUCCUCGA
UACGCUAACCAAAAGAUACAGUAAUGUUUGAAGUAACCCAAGUACUAAUGUAAUACUAGC
AGAUAUCAACUAACAGCCACACAUAAGAGCAGAUAGGUGAAGCAGCAACAGAUGUACAGC
AGUCCAUGUAACGAAAGAUUUCAGAAUCUGCAAUCAGGAAAUCACCACAACCAUUAAAAG
CAUGUUGCAUCCAAGAAGCUCUCAAGACACCUGAACAGAUAUCCAUGUACGAUUCAAUCA
UUCAAGAUUCCAACAUAUAAAACUUGUUGCAGCACAAAUUUCUAAGAUAAAUCAUUUUCA
AAGUAUAGGGGAUGGGCAUAAGCCCACACUAAACAGCAUACUGCGUCAAGCAAUAAGGGC
UCUAUAGAACAUGCAAUAGACUAGUGCAAGUAGAUCCUCUCCGCCCACUAAAGGAAAAUA
GUCAAAAGAGGAAAGCAAUCUCAGACUAACGAUUUCAAUACUAAUUACACAAAGACAGUU
ACCCCGUCCACCAAUACAGUCUAUAAUGUUCUGUUAGCUUUAUGGUUUUUCCCAAUUGCU
AUCAAAUAGAAUGGGGUAGUGCUUGAACAUUAAUUGGGGCAGUAAAAGUUACCAAUACAC
AGAACCAAAGAAAAAUAUCUAAGACAGUCCAUUAUAUCUUUCACCCAAUCCCAUUCCUUG
AUGAAGAACUCACACAAAAGGAGAAGCCCCUUACACAUGGAAGUAAUGCAGUAAAACGGC
UUACACAGUCCGCAAACAAAUUCUUGUUAUGUAAUAGAUGUCCAAAAUUUACCAGAAAUA
UCAUUGAAAAAAUCAACUGAUAUCCAGGAGCCAGAGAAUCAGUGGUAAAACAUAUGAACU
UUCCACUCUGCAGCCCCCUCCAAAUGCUUUAAAAACACACACACAAACACACAGAAAUAG
AUAUUUGUGGAAUUCAGAAAUAGAGAAAAUAGACAUUAACCCAAAGUACUAACAAAGAAC
ACAUUGAUUCCUGACUUGUCACUCAAGCACACAAUUUUAUUCUCCCGGACUCAUCACAAA
AAUCAAGUAAUGCACAAUCUACACCACAAAAUUGUAUGCAUAGCAUCGAAAAAGGGUGGA
UACGUUACUCAAGAACAAGCAUGGCCAAUCAGAUCACCAAAUAAACAAAGAGAACAAACA
CACUAAUUAAGAAAUUGUAAGUCAUGCAGUCUAACAGAACAUUUAAACUACACCAUAUCA
AACAAGAAAAAGUAAGUUGGUAAGCCAAGACACCUAAUAUAGAUGCUCAACAAAUAUUUG
CAUAAAGAAUACUAAGUGAAUCAUAUAUUGACAUGCGUAACUGUCAAACUCACAAUGAUC
ACCUCAGUAAUAUGGAGGGAUGCCCUGGUACAUCCCACCUGGUGGAACCCUCGACCC

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 [-721.66] kcal/mol.

2. The frequency of mfe structure in ensemble 1.3286e-44.

3. The ensemble diversity 755.54.

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