lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-569.20) is given below.

1. Sequence-
UGUCAAUUGCAAUUCAGCUAAAAAUUCCAAUUCUUAUAUGUUGUUUGUCCUUUGACCUUU
UCAAUCAACAAUAAUAGAAUGACAUAUUUUUAUACAUUUAUUUUUUAAAUCUUAAUGAUC
UUGUGUCACAACCCGAAAAUCGAGUUGUGACGGCGUUUACAUCUCACCUAUAUAAACAAG
UCAAAUUCUUGCCAACGCUAUAGCGAUGGGCCAAUAACAAGAACCCAAAAUAAAAGCAAA
GGGAGGAAAAAAAAAGAAGAGUAUAAAAGAGAUCUGAAUUAUAAAAAUCAUUCAUAACUC
CAAAACUUGGUGUCAUGGCUAUAGAGUAUAUAUAUAUACAUGAAUACAAAAUACAACUUC
AAGCGGGGCAAACUAUGAGAAUUGGUUAUCGAAGACCUGACUAGGAUAGCUCCCACAUUG
AUAGAAAAAUUGCCCUGCAAGGACGUAAGCUGCUAACCGAAUCUUACCAGCUACUGCACU
CGAUCACGUCCGAUGGUAAAAUUCGUAUUAGUACCUACAUCAGGAAAAAUUGUGAAAGUG
UAGUAUGAGUACCAAAAUAAAGGGUACCCAAUAGGUAUCAUAGGCCGACUAGGCAUAAGC
AAAUAUAAGCAAGAUAAAGAACAAAUUCUAACAAGUAACAUAGUGACACGUAGUGUAUAA
UUGAAAAGAGGCUACAAUAAUAGCUAGUAAGUGCAGCAAAGGAUUUAUACCAGUGCGCGU
GUAGAAUCAGCUAACAAAUAUAAUAGAAAGCUACUAACAAGUUACUGUAUAUAGACUCGA
GUCACGACCAAAUCAUGACUAGACGGGACACAUACCUGGAACUCCAACGUAGUCGAAUCA
AGGAAAUACUUGCAAGAAAUUACCAAACAAUCACCCAGUUAAGCUAAUCACGAACAAACU
AGUGCAUGAAUAGUACUAAUCAGAAAAAGAGGGAUACAAGUAAAGUCUACUAGCAAAUGA
AUCUAGCCUGUAUCCCAUUCUAUCGGUAGGUACACUCAGACAACCGAGUAACUCAACAAG
UACUCUCCCCUUAAGUCCCGAAGGGUACAGACAAUGCGUAAGAAUGCAAUGUAAAGGAGU
GCUGGAAUAGUAAAUAAGUGUCCGUACACAUCCUCCCCGGUACAUGACUAAGCCAGGAGU
AGAUCCACAGAAGCUAUCCCAUAUGCUUCCCCAACCUCCCUUAGUAUACCACUCCCCCAG
CUACACAACAUACCCCAGGCUGGCGACCUAGGUCAGAAGGACCAUUGGGGGAUCCAAUCC
CACGUAUAUAAUUCCUGUAAAAAGGCACCUAAUGCCGUAAUCCUCAUAGCCAAAAGGGCA
AAAUUCGGCCUUAACCCGUAUAACUUAUCUUAAUAGAUAGUCAAGUACAGUCAUACAAGC
AAAAGUUUCAGUCCAUAGGCAAGCCCAGAAAUCACAGUGAAUACGAGAAAAUAGCCUCAG
AUAGUGUGAUAAAAUAGCUUCAUACCGCUCAUAAGCGCAGUCGUGGAAGCAUAUAUGAGG
CCAGUUUUGGGUAAUUGCUUUGUCGAAAAUUCAGUUAUCUUUUUAAACUUCAAUGCAUGC
UCGCAACACAAAAUUAAUCAAUAAGUUAGGCUAGUCUAAGACUGCAAACUAGGGCCCCUA
AAAUAAUUGCCAGACCCCAACUCAUAAAGGUACAAUCCUUCCCCAGCCCUAGUCCCGAUC
UCGAGCCUCGAACACUUGCAUCCCAUAUGCUAAGAUGUCCCUAAGGGCGCUUAUCAAGGG
CAAAGUACACACCCUUACCGAGAAGAAGAACACAGAGCUACCAUAGCUCAGUCUAAAACA
UUCACGUCCGAGCUCGUGCUGGACUAGGGAGCACUAUCAUCAAACAGGACCCAACCAAAU
AGUGGAACAUUAACCGGCUAUCCAGGCUCGAAUGAACCAACCCUAUUCUAAUCACAUAAA
CAACACAAGUAGAGCACAACAAAAUAGCCUACCUAGAUCGGCUUUAAAGCCACAAACCUA
AAUUGGGGAUAGCUACUAAGGUCUAAUACUAGUUUAAUCCUCUUCCUAACCUCAUUACGG
UCCAGAGUCCGUGUAUUAAAUUUGCAUUAAAAGUGUUACUCCUUCCCCAGCCACACUACA
GUUCAGAAUCGGCGUGAGACACUCGGGCAGGGAAACACGUCCCCAGGGUAAGUAGUUAAG
CUACAAGCCAGCUAAAUAUGUCAAAGGCCGGAUAAAUAAGCACAUCGAGGCCCGAAUAAU
CAUCCCAGACCCGAGCUAGGGCUAUACUAAUACCGAAUCUAGAAAAAAUACACCGUAGCC
UACCUGGUAUCCGGUGAUAUCCUCGAAAAGCGUGCUCUAAAUGCUCAAAAUUAUGUACGA
GCUCAAAAUCACGUAAGGCUAGCAAAAACAUAACCUACGCGUUAAUAUGAGUAAAACAAG
ACUCAUAUUGCCAUGCUAUGAUAUACUUAUUCCCAUGCUAGAGCACAGCUCGUGCAUUGU
ACGCUACAAAAUAUAGCUAAAUUUAACGGUAUAAUUGAAAGAUAUAGGCCAGGGAAGUUU
AUAUAAUAAAGAAAAAAAAA

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 [-609.76] kcal/mol.

2. The frequency of mfe structure in ensemble 2.63191e-29.

3. The ensemble diversity 622.21.

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