lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-550.20) is given below.

1. Sequence-
UUUAUGUUAUUCCUCUCGUUCAAGCACCUCAAUAUCUCCUUGGAACAAUGGGAUGAUCUU
UGCUGAGUUGACAGUUAUGAUGUAUGUAUUUACUUUGCCCUAUUUUGUCUUUGAGGCAUA
AAUUAAUUUUGUUUGCUGUUGUUGCACUAUUUCAACCACCUAACUAUCUCCUUGUGAAGA
UAGGUUACUUAGAGUAUUUGCUGUUGUGAUGUAUGUAAUUGCUUGGUCAAUCUUGGGUGC
UCUUUAGUUGGUAUGUGUUAUGUCCUUUUGUGAUGAACAAUCCAUGGCAACCCAAUUUUU
UUCUUAAUACUAUUUAUACAGAGCUAUUAGGAUCCAUUUUUCCUAUAUGUGCAUAAGGAG
CCCAUCUUUAGACUUCUGUAGGUCACGUCAGGUUGAUCGCUGGAAAAAAUUGAAAUUUGA
AGCCUAUGUAUCAUAUUCCACUUCUUGCUCCAAUAAUGUUUCUGAACUGCUUGAAGCUUA
UCAGUCGUGAUACUUUUAAGGAAUUUACAAUGCUGAAAACACAUUUCUUCAUGUAGAUGG
UGAUAAGUGCUUAAAGAGGGGCAUAUAAUUUACUAGUCUUUCUUUUAAACGAAUGCUUUC
UGUUUCCUUUUUCCAUUUUUCCUCCAAAGAUAUGUUCUAGCUAAUCUGCAGAGGGGCUGA
GGAAACUUAAUUCUAUCUUUAGUUUUGACAUCCUUUUUGUUUUCCAAGAGGAAGACAUGG
UGGAGGGAGCAGUUUACAUCGGUGGGCUGGAUUAUAUUCUGGACCUGGGUAGUGAAGGCC
UGAAAGAUGACCGAUUAAAGCCUACUUUAAUAGAAUCUUUUUUAAAGCUAGAUAUGGAAC
GUUAAAUUAUUUGUGUUUGUAUUGCUUAUAGCUGUAAGAUCUUAUUUACCCAACUUUGUU
UGUUUGGUAAGUUUUAUCUGUAUUUCAGGUCUUCUUGAUGCAUAUUAUCAAACUAUGCAG
AUUGGUUUGUCGGUAAUUCUUUUUUUACAGUGACGACUUUGAGGGUCUGGUGUCUUAUAU
AGGUUUUUUCCGAGGCUUAGCUUCUUGCUAUUUGCAAUUUUUAGAGCAAAUGCUGCACCA
UCUUGUAUUUCAUGCAUUUCUGAAUGAACUCUGCAAGUUUACAUGAAUAUGAAUAGAGAC
CCUUCUCACAUUCAGGUUAUUUCAGAUUCUUAUAGUGAAAAUUAGUCUAAAGUGUUGUGA
UUUCGUUAUUCGGGAUAUUGAUGCAAUUACGUUUAAUUUUCCGGAAUACUUAGUAGCAGG
CUAGCAGCUCUUAUCUGAACAGAUAUUUGCAGCUCAACCAUUUUUCUUGUACAAAUCAAA
AGUCAAGGCAUGAUAUUUUUUAUUCAUAUAAGCAUGUCCUUUAUACAUAAUACCUAAUGC
UCAAAUGUUAAUGGGGACUGCCAGUAUAAUUUUGCUACAUUUUGUUCUAUUGAUCUUGCA
GGCCUGUUGAGUGUUGACUAGAUGGAUGGAGGCUUUCAUGUGGUAGUUGAACAUUUUGUA
UGCUUUGAAGAAGAGGCUUGGUUAUGGCUGACAAGGCAAGUAAUGAAGCUUCAUUUCCGC
UAGUUUUGUCCAGCCAUCGCUUUGGUUUAUUAUGGAUCUCUGUUGAUUUGACAGCAAACA
GCUUAAUGACCAUGAAAGAAUCGAGUCUGCUGACACCUUAUUUACACUUCACUUUUCACA
GUAUUGUUAAUUUUUUGCAGUGCUCGGUAAUCCUAUCUAUUAAUUGCUUCCACCACCUGC
UAAUACAAGCUGGUUAGUCGCAGGAAACUGAAAGGAAUGCAAUUAUAAUGAAAUAAGCGU
AGCAUAUUUUCCAGUGCUUAUAAUACCUUGCUUUUGGGAUAGAAAUUCUGUAAUCUUGUA
UACUAGCUAGUAGUCAUGCUUGUUCAGUCUGAUAAACUUUAUGAUGAGUGAAAUACGCAC
UCAAAACUUUCCGGAAGUUACUGAUCUACUUGUUUGUUUCAGAAGCUAGCCAAUGCCUCU
CCAGGUUUGUAUGCACGCCAUGCACUUUAUUAUCCCAAAUUAGUAUAUGAAGUAUGUGCC
UUGGUCAUCUUUGAGUAAGAUUAGGUCCGGAUGUUGUUCCAAGCUAAGAUGUACAGGUUU
UUCACUCUCAAUGUCGCACCCAUGUUUUAUUUUUCAAAAAUACAUUACUUUUAGAACUCU
GACAUGCAGUCCCAGCAACAGGUUCCAAGUACCCCCAAGAUUCUUGGUGGUUAGAUGAAG
GUGUUAGUCUGAAAACCAUUCUUCAUGUUGAAGGCGACUUAAGUUUCUUAAG

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 [-592.49] kcal/mol.

2. The frequency of mfe structure in ensemble 1.58964e-30.

3. The ensemble diversity 561.43.

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