lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-499.30) is given below.

1. Sequence-
CUAAUCUUCUACAAUAACGGCUGAAUUCAUUACCCUGAAUGUGUUUUUUUGGAUAAAUUA
UCUGUAUGGUUUGGAUUAAUUUAAUGCGUUUGAGUAAAUUGACUAGUUAGAACGUGAAUA
AUACCUUGGUUAUUUGUUUUGUUUCUAGUUUGUUUUAUUCCCUAACAUAAGUUGAACCUG
UAUACAUAUGUUAGUAGUUUUAAUAGUGUAUAAUAUGUCACGAUUUUCUUGAUAAGCUCU
UGUUUGUCCUAAAGAAGUCUAUGUUGUACUUAAGAUACCUAACUGCUAGCGUGAUACUCA
UUCCAAGAUCCUGUAUGUGAGCUUAUUUUAGAAAAAUGUUGUUCUGUUGAAGCCUGUGAA
GUCAUCUGUGUACUAUAUAUUCUCAGAUGUCAUAAUCAAUAAGAACACCAAAGCUAGUAG
UUGUUUCCUUAAUUUCUGAGAUGUAACACGUAUGCUGCUCAUUGUGUUCUUUAAGAAUGA
ACCUGCUUUCUCUUGGUUUAAAUGUAAAUCUUGCCAAGACCUGAGAAAGGAGUCUGUAUU
AGGUUUUUAUUAGCCUAUUGAACCUGAUGGUUUAAUGUGUUCUGUGUUAUCCUUGCUAAU
UGGCCACUGCUUAUACCUAUCUAUGCCCACACGCUUGAAGACUUGCUUUCUUUAGCCUAG
AACUAAGUAGCUCAGUCACCUGAUUUAUGGAUUAAGACCAGCUCUGUUUUCUCUAAAUUC
GCCUGUUGAGUCUGUCUGGACUAAGUUAAAAAUUGGACAGAGUAGUAUGCCUAGGUUUCC
UCUAAAUAGAAUUCACCUAUUUAUCCGCUGCUUAUACACUGGUUGGUAAAAUAGGCAUAA
AAACUAGCUUUAACCACUGUUAAUAGCAUGUUUGACACAAGUUGGUAAAUUUAUCUUGAG
UAAAGUGUAGAAACUGGGAAGAGUAUGCUGACAGUUGUUUUGAUGAUGAACUUAUUGACC
AAGGAUUUAAUUAAGAGUGGUGUUUUGUCCAAGAUUGAAUGAAUGAUAUAACUUUUAUCA
AUAGCAUUGGACCUUUUGAAAUGAAGGAGGACAGUAGUUGCAUAAUUUUGAAGAACCCAU
GAACCUUUUUCUUUCAGUAACAUAAUAUUUAUCUUUCAAGCAUGAGCUUGUUGAUAUAUC
AGUGCCUCCUUGAGUAGUUACGGGCCUUGUGUACAUAGUUGGUAUUUAUUCAUUUUGAUA
ACUGUCUUUGAAUAUCUACAAUGGAUCUUAAAUGCUUCUGAAUCCUGAAUUUGCAAAACU
UGUCCUAUGAUAGUCUGAAAGAACUAAUUCGUAUGUUUUAGAACUUGGACAGAUUGUUAA
AGCAGGAAACGAGGAAAUCUGUUUGUGAAAUUGGGAAUCUAUUUAUGUCUAAACCAGUCU
AAUAUGUAUCUUGGUAUGAGUCAUGUAUUAAUGUGAAAGUAUAGCUUGGAUUACUUUACA
UCAUUGUCAUGUAAGGCGUAAACCUGUCUAGUUACUUUCUUUCCUUACCUUCUGGAUAUC
UAAUAAUUGAUGUGUGCUACCUUUCAUUUUGUUUGCACAUUGUUUGAGCAUCCAUCCACC
UCAAGUGACCUUGGUCCUCAAUAAUCAAAUAGGGUCACCAAAUAAGAGUUUGGGGUUGCU
CUUCUUUGUUUUCAGUCACUAAAAUUAGUUAGAGAAUCUUGUUAAUAUCUUUUCAGUGAU
UUGAGGACACUAUGUGGAAUGUUUCCAUAAGAAUCGACCUUGCUUAGGUCCAAAUCUUCA
CUUUUUUGCACUUCGUCUUCUUUCCUUUGUUGAAAGUAAAUUGAAUCCAUAUGGCUUAAU
GAGUUUGAAACUUUAAUUUGGAGGGUUUGUUUAGCAGAGUGAAACUUUUCUGCCUUAGCU
UUACAUAUGUGGGUAAACUUGUAUAAGUAUAAAAAUGUAUGACUAAUUGAUGUAUUAUCC
AUUUGAUUCUGUUGUUAUUUGUCGUUUUUAAUUCUUCGAUAAAGGUGCACUGAUUCCUUU
UCUUUUCUUGCAUGACCCACCCGUAUCCGGGGCCUUAUGGACCUUUCCUUCAUUUUGAGA
UGGGCUAAAAUAAAAGCGAGUCGGACUCCAGCCAAGCGUUAAAUAAGCAGAAGAAUUUAA
GAAAGAUUCUAGUAGGAUCAGAAAGACGAACGUAAUUGUGCGAGAUAGUUUGGAGUUGUU
GCAAGAGAUACGGUGAGCAAUUGGC

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 [-544.76] kcal/mol.

2. The frequency of mfe structure in ensemble 9.3059e-33.

3. The ensemble diversity 494.83.

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