lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-718.50) is given below.

1. Sequence-
CUAAACUAUACACACAAAGGAGAGAAAAGGAGAGGUUGGGUCAAGGCAGUUAGGCCCGAA
CACCUACAAAUAUCCAAAUGGGCUACAAAAUAUUUUUUGGAGUUAAGCCCCUUUACUUUC
UUCUUCUGCUUCAUUUGGCCGUUCCUAUACAUUAGCUUCCUUCCAUAUAUCAUGCAUUAG
GUCAUUUCUUAUUUACUUGAAUCUGGACUUUGAGAUUUGAAUCGAUGGAAGCAUUGAGUU
CCAGCUCAAUAUGCAUGAGAGGAGUAAGCCCGGUUUAGACUCGAGAGGGUAUCACAUGCG
AAUAAAGAAAGAGAGAAGAAAAAGAUUAAUUACCUAAUCAAUAAAGAUGAAAAUACUAAG
UUGAACUUAUGCCAUUCAAGGUAAAAACUUUGAGAAAGAAGAAAACAGAGCAUCUAGUUA
AUUUACUAUCUCAUUAUUCAAAAAGCAUGCAAAGGGCACACAAACAGAAAAAGUUUAUUU
CAACAAGUCACACAUGUUGGUUUUGGCAUCAAAUAGUAAAUUUCCUCUUAAUAAACAUGG
UUGAACACAUAUUAGCCUAGAUAGCUCUAAUUCCUUUACAUGUCUUACUAGAGCUCGAGC
AUACAAGGAAAGGCCAAGAGACACUUUUAGAUUUAAAGGUCCCUACUUUAAUAAAAGUGA
GACUAAGGCAGUUAUUUAAAACUCACGAGUGAUUAGUAAAUAGGAGAUAAGAAAGCUACU
UCUCCUUUCAUACUCUUAGGGUUAUCAUGGCUAUAUCAAAGUUCAGAUAUGAGUAGAUGC
AAUAAAACUGGUUCGAUAGUUAAUUCAGGCAAUUGAAGACUCGAGCAUACCUACAUGCGU
CAUCUCUAAAAAAGCCAAAGAGAACAAAAAUUUGUCCAGGCAAUAUGUUUUACAGAAGGA
GCAUUCUAUGCAGAAAGGAAGUACCAUAACAAGCCCUAGAGUACUUGGACCUACAUAGUA
UGCACAUAAAAAGCAUUUUCAAGAUUUAGACUUCAAUAACCUAAGAAACGGGUUUCCAAG
UCAUAGGCUGAAUAACAAUUGGAGAUCAAACGUAUGACCAUCGCAGAAGACUCCCAAACU
GAACAAAUCAAUACAUAAAAAUAUGGUGCAUGUUAAAACAAGCAAAUAUGAACUGGAAAA
UUGACUUAUGCAAAACCUAGUCAUGCUCCUAUCAUUCAGUAAGUUUGUGUUGCCAAAGAA
CCCUUAAUGACUUAAACUCUAACACAGGGAAAAGAGAUUAGACCAGUCAAUAACCUUAAA
CAUGUUAGUGAUUCAGAACCUAGACAACCAACUUAAAAUUAAGACUUUCCCUGAUUACCA
CUCAAAUGAUAAGUCAUAGCACAACACACCUCACACUCAUUUAAUCAGCUAAGAAAUAAA
UGAAGAUGCAAAGAUCAUGUUGUUCAGGGCAACCAACCAUGGGAAUGGGUCUUGAAAGAA
UACUUGGAGAUGGGAGCAAUCAGCAAAUUACUCUAACUCAUUGGGACAUGUAACAAUAGA
AGUUGAACCCUAUACUAAAGAAAGUAGCUUGGACCUAAACAGAUAAUAAUGAAAUAGUCA
CAGGAGAACACUUAGUUAAUCAAGAUAGCAACCAACACAGGUUUUAAGAUAGUUUUAUUA
CACGAUGAACAUAUGAGGUUAUUAUAGAGCUGGUUAUAGCAUUUUGAUAUCACAUUUUCA
CCUAACAUACAUGUUUAAACACCCCAACAACAACUUAAAAAAAAAAAACUCUAGUAGCCU
AUAAUGAUGGUGACUCAAAUAUGAAAGGAGUACAACCACUGGUAAUUAGCCAAAAAAAUC
UAGAACUAAGUUCAAAUUCCUUGUUUUAUCACCUGAACCAAAGAAAUAGGUAGGUGACAA
GAUAUUAGUCAUUUGUGGACUCCUCUACUCAUUUAUAAACCUAGAUAUCCUAUUAAGCUA
GUUAACAUGCAACAAUACAUAGAUCAACAAAUUUCCCUUAAUACACAUACCGGGACAAUU
AAGAUCAACUAGAAAAUAGCAUUGCAUAAAAUCCCAACUUUAAUCUGAAACAGUGGUUUA
AAACAAUCUAAACCCUAGACAAGCUACUGCAUGCUGAAAAUAAUAAGAAAACUCAUUUCA
GACAUAAACAAGCAUGUUCAUGCUCUUCUAAUAUGCAAAACAUAGCCAGGAUCCGUUAAG
CAUUCACUGGUUGAAUUAGAUAACAAAGGGUAACCCUAUCUAGGAGCAAAAUACAGAGCU
GGCAUGCUUAAGCAGUCCAGCAACUAAGUGCUUUGUAAUUUACAGUUUGAGAGGUUUAGG
CAAAGAAAUGGAUUAAACACACUAUUAGAAGGGAACCAACUUCGUCUAUCAAGAGUUCAA
AAGAGUCCUAGUCAUAAAUAUGCCAUUUUAAACAUGAACAUAGUAAAUGAGGCAAUCAAA
UCCUUUCAUGGUGAUUACAUGUUGAUUGAAUCACAGAAGCUUCAAACUUUAGCCUAAAAC
AAUAGCUUAGGGCAGUGCAUUUUCCUAAAUAGCUACUCAUUUUUUAUUUUAACAUGAAAG
GUGCUCACUUUUACUCAGGCUUACCUGAUCAUGUUCAAAUGCGAAAGACAUUGACAAACA
AGUCUUCACAGUGAACAAAAAACUCAAGUGUCUUCAUAGUGAACAAAGAACUCAAGUAAA
AUGAAGACCAAAAAGUCAUAUUUUCACUUAAGUUUACAUGAUUACACCUUCAAACAAUAA
CUCACAACAAAGAACUCCCAAAUACUCAUUUGAAUAGUUUGAAUAACAAAAGGUAGGGGU
CUCAACAAAACAGUGGAAUGUAUAUAGCUAGUUCAAGACAAACAAGUUAAGAAAACCCAA
AAAAUAGCCAUAUUUUACUCAACUAGGCCAUGUUUAUGCUUUAAAACAGUAGACCACACC
UCUAACAGUCAAUUCUUCAUAAACAAAACAAGAAAAUGAGUCAGACGGAUGAGCAUUUUA
CCUAUUUUUGAACAAGACUUUGAAUUCAAGGAAAAUUGAGUGUUAUCUCUACACUAUUAA
GUGAUAUCCAGAAUGUUUUAAUCUAGAAUUCAAAACUUCAUCCUUCUAACACCCUUAUAG
AUGUAAGAAAUGGCUGUUACAUACCCUGAGGGUUGAGAAUCACUUUACCCUUACCCUUUU
UAUUUUUUAUUUUUUUUGAUGAAAUUUGUAUUCUAAGCUAAUAUUAGGUCUGAGCAGCCC
AAAAAUUCUUUUACCCUAAAGAAAAGCCUACUAUCUAUUGUGAAUUCUAAAACUUCUGAG
ACUUAUCGACCAAGACCCCCUAAAACAGUGAAGGGAAGAGGCCUUAUAUAGAAUUCAAGG
UAUGUGAAUAGGGGAGGAUAAUAUCAGGGAUUUCUAGAUUGGGAUCAAGACAAGGGACAA
GUGGCCUAAUCCAAAACUCAUUUCGUGCAACAAUCAAGAAUUAUCAGUUGAUUCCUAAAU
CUAGGGUUAGCAAAUUAAAAAUUCAAACAGGAAAACUCAACCAACCAAUCAAAUUCGAAC
AGCUAAGGUACUUAUCAUCACAAAAUCAAAAAGUAAUUUAGGGAUAUUAUCGUUGGG

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 [-782.15] kcal/mol.

2. The frequency of mfe structure in ensemble 1.39719e-45.

3. The ensemble diversity 675.09.

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