lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-241.40) is given below.

1. Sequence-
CCAUCACAAAUUCUCAUCCGCCUGGGUAGAUUAUUCCUUCAAACAAAAAUUAACACACAU
UACAGGAAACAGAGGCCAUGAAAUCAGCUUAAAUAUGUAAGCAAACACAAUUCAAGCCUA
AUCAUAUCAAACCACCAGUAAAGCAAUUCAAGUAAAAUUUCUUAAAGAAAUGAGAAUGUU
UGGUCUGUUAAAGCAAAAAAAAGUAACCAGAUAACCAAGAGGGGUACCUAGUUAAUCAAA
UUGGAGAUAGCAAGUGCCUUAAGCUAGGUGACUACAUUACACAGAGACAAGAAAUAGAAC
UACUAAAAUCGUUCACACCAUUUACUUUACUUAUCCAGUUAUAUCAAGACAGGGACUUGA
GCAAGUAAAACAACAAUACCAACAAAACAAAAACAACAUUUAGUACUUAACAGACCAAAC
UUAGUUAGCCUGAAAUUCACACGCAACUUCAUAUUCACCAGUUAACAAAGGCACCAAACA
CCUACCUGGAACCUACUAUAAUCGAUGUCUAACCAAAGAUAUCAAGGCUAGGACAUGCUC
AUAUCUAGAUAGAAAACAAGAGAGAAAACAGUAUGUUUUGAAACAACGUACAUGGAUACC
CAGUUUAGAACUUUAAACAGACAAACAACCCCAAUAUUUCCUUUUCAAUAAUCCUAAUUG
GUAUUGAAACCAAGGAUAUUACAGGAGAUCAAAUUAGUACUCAAGAUAUUGCAGAUCAAA
ACGGAAAUAUGACCAGUUCUUAUCAAAAUAAUGAAUCAUAAAGCGCUAUACUUCCAGUAC
AAGCUGAGAACAAAAAAGGAGACAAGAAAGAAGUACCCAUUGAUCUAUACUCCUAAAAUU
CUCUUCAAACAGUCAUAACUUAAAACCUUAAUGAAACCAAAAGGCCAAGUCUAAACCAAC
AACAAGCUUGAAACAGAGGAAGGAAGUAGAAAGAUAUCCAUGAAUAGGUUCAAAGGAAGU
CAAGUGACCUGAACCAUUAAAGAUUAUAGAAAAGAAAUGACGAGAACUCUAAACCGGCUU
GUAAAUAUUUGACAGUAUAGCAGACCAGUCAUGUUCAUUGUUUCGCAAUGACAUAAUCGU
GAACAUGGAGGCUUCAAACCAAGCCACAAAUAGAACACUCACAAGGACUGCAAUUUAAAC
AUGAUCCAAACGGCUUCACCUUAGUCCAAAACAACCUAGGCAAGCUCCUAUACAAACACA
CUCUUUAACUAUAUAACAAUAUAGUGAAAACUGUCAAAAUAUCCAGCCAUUUCAUGGUCU
AAAGCUAAUAAAUUAGGCAUAGGAGAAUGAUCAUUUUCAUGAAAAUAAAAGGAGACGGGA
GAAACUCCAAGUAAUGGCAGGAUUCUAGAUUCAAUCAAG

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 [-265.45] kcal/mol.

2. The frequency of mfe structure in ensemble 1.12475e-17.

3. The ensemble diversity 252.51.

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