lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-612.40) is given below.

1. Sequence-
GUUUGUUUGGUUUGAAAUCUGUGAGCUAUCAGUGAAAAUAUAAGGUCUAAAGACUGUAUU
UGGUUUUUGAUGUGUUUUAAGUUACCAAUUUCCGAUGAUUCUUCACAGUUUUCAAUAAUG
UACUAGUACUAUUAGGAGAUAAAGCUGAAAGGGAUCUGUACCUUGGUUACUUUUCCCUCU
UAAGGAUUAAUGGGUGAGGGAAGCUGCAUGAUAGCUUAUUUUCACCUUUAUGACUCAAUG
GAUUAAUUUUUUAUUCUCCAGUUUAAAGAGUCUUGGUGUCUACCUAAAAAUUUUAGAUAC
UGUUUGAUUUUAGAGUUCUCAAGGAUAUAUUCAUGUGUUCUUGAUCUAGUUUGUAAGGCA
GUUUCUUGACCUGCACUGUGUGAAUAUUUGUGAGCUCUUGGUUGUUGCUGUUGCUUAUUU
GAAGUAAUGAGCAUGCGAGCCCAUGUUAAAUUUGAGAUUUUUAUGACUUAAUAAGGUGAU
GGCUAAUGCUUCUUACUGUGUACGAAGGUAUAAUAUGCAUGCUUAGGAAGAUGCGACUGG
UUGAUGUUCAUUGCACUAAACUUUGUCUACUAUUCAAAACAUGUUCAAAAUACCUUGUGU
GUUCCUUUUUGUUACCGAAAAUUCACUCUUUGUUGUUUUGAAAAUGUUGGAGUGUUGACU
GUUUGCUUUGUCAUUUGAAGGCAUGAACAUGCAUGUUUAGAUAUGUAUAAAAAUGUGAAU
GAUGAUAGUAGCAUGUUUAGGAGUAUACUUUCCUAUUUUUUAAUGGUUGUGAGUAUGUCU
UCUCUUUGAAGCCUUAGUAACAUGACUAGGUGGUCUGCCUACCUGAUGCAUGAUUUUGAC
CUGAUUUGUUUUGGUGUGAAAUCUAAUUUAGUUCAACUUUUUCUUUCUGAAUCCCUCUUU
AUGGUUGAAAGAAACUGACAAGUUUGAUCUUCUAUGGAUCAAGUAGCCUUCUUCCUAUGU
GGAAUUCUAAUAUAUCAAGAUGACCUUUUUUUUGAUUAAUCAUAACCUGCUUGAGGGUCU
AAAUUCUUGUUUAAGUCAUACAUGCUAGAAGUCACUUCGUUUAGGGUCUGUCAACUGGAU
ACAAACUGGUUUGCUUAAAUGUCCUUAAAAGGUAUAUCAUCCAGUAUGCUCUGGGUUUGU
UUUUGAGUUGAUGUGGUUUGUAUGUUAUCCAUAUGAAAUAUGACUGCACUAGUGUGAUUU
CUCUACUUGUCAAUUGAGAACACACCAUAUCCACCUCACUAGUUGAGAAUAAUGAGUCAU
GUUGUCAACUUUUACUGUUUUGUGGUUCUAGUCCUUACUUGAGCAUCUAGUAUUUUAGGC
UUAAUUGAAAUGAAGCAAUUGUCAUGAGAAAUUUGUAAGUAGUAGCUGGUCUUAAGGCUA
GACUGUUUUAGUUGUGGCUUCCUUGACUAAAUGAGGAAUUUCGGUGUUAAGCUUAAUCAA
UAGCCUCCUGUGUAAAGCACAAUUGCUUCAAAUCCCAUUCCACGUUAAAGUUACAAUCUU
UAAGGGGCUGGUUGAUGUGGUCUAAUAUUUGGAUUCUUUAAAAUGUGUGUUUCUUUUUAU
GGAAAUUGACCUCUUAAUGACAAAUGUUGCAUGCAUAUCUUCUACGCCAUUUACCUUCCU
UUGAAUAGCAAAGAACCUUAAAAUCACUGUUAGCGGUCUAUGCAAGAGUGGACUGCCUUA
GCCUUCUACUAUUAUGUUUAAAGUUGGAACUUUCGAGUCCAUGAAUAUUAUCUCAUCUUU
CCUGGUAUACUUGAUCUCUGGCAAAUAUGUGAAAGAAAUCAUCUAGCUUCCCAUUUUAAA
ACUAGUUAUUUGUCAACUGGAGGACUUUAAUCUUGCUAAGAUUACUGCCAUUGUGGGAAG
UCUACUUUGUUCGAAUCAAGAUUUGAAUUUGUUAGCUUACAUAUGACGUGUGUUGUAAGG
AUAAAUUGGUUCCAGAAGUCCAUUGCUUGCUAUUAAUGACAUCCAGUGGUCAUUUUAUUG
UGAUUAAUUGGGACGUGUUAACAGUCCUUUAAUUUAGCUACUAUUUUGAAUUUGCAACCU
GUCAUGUUUAGAUGAAAAUAAGGUUAUUUGAAUGGCUACGAGUAUUUAGGAAAAUCUUAG
UCAUACUUGACUGUUUGAAGACAUGGACGUAUGUGCUUUGUCUAACGGCAUGAAAUAUUU
UACGAUAAAUCAACACUAUAAUAUUUUUGGAAUCUAAAUGUUGAUUGAUUAUUUCCUUCC
CAGAAAAUGCUGUUUUUCAAAUACCUCUGCAUUUUUAUUCUUUGAUAUCGACUGAAUUCU
AGUUUUUCAUUUCUUUCCUGUGCAUGUGACCCUUCCCUUGAAUCCAUCAUGGAUUUCAUU
CCUCCUUUGCGUCAUAUCUCUUCGAGUCAAACCUUCUCCGAGCAAGAAAGUACGAGAAGA
AACAUAAGAGAUGAUCUAAAAGUCAUAUGUGAAAAGCAAUGAAAGUGAAUCAAACGUACA
GGGUCGAAGACGGAACGGAAUUUAAAAUGGAUUUAACCCUAUAACUUUGGUAGUCCGAGU
UGGACAAUUGUACGGUUUGGGUCCAAGUGUCUCAACUCAAUUUCUUUCCUUCUCUUUAUU
UAGUUACUUG

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 [-666.14] kcal/mol.

2. The frequency of mfe structure in ensemble 1.35577e-38.

3. The ensemble diversity 766.10.

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