lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-628.40) is given below.

1. Sequence-
UGAGCCAAUUAAAAUGAAACACGAGUACAAUGAGAAUAAAAUUACAUCUUCAAAUAGAAU
AUGAAAUUUCCAUGGCUAAAUAAGGAAAAGGUACUCGGGAGAAGAUGAAAAGAAUUUAUG
GCAGCCUUAAAUAUCAUCAUCUUCGUUAUCAAACAUAUAUAAAUGAAAUAGCUUCCUAAG
GGAAUGACCAUCCCUUUCUCUUGAAUGCUGAAAACAUCCUCUCAGUUUUCUUCCAUAGUU
UCUCCUUAAUGACAUUGCAUUCUUUCUUCUCAAAAGAAUCAGACCAUGUUUGCUCAAAAA
UAAUGAAAUGGAAAGUAAAUUUGCACAUGCCAGCCCUCUUUACGUAUGUAGCAAACAACA
GUGCCACCUGCUUAUUUUCCCACUACAAAUUUUGAGGUCAAGUUGUCACAAUGGAAAGGA
UACAAGAAGGCGGCACAUUAUGCCUUACCAUGCUCCAUUAUUUCAUCAUUUCCUUCUUAU
UUCAUAAUCCUUCAACCAAUCGACCACACUAUACAAAGACAUUGCUACAAGUCCACAGGA
CUCCAAUUUGACACCUUCUAUAAGAGAUUAUCCAUUAUGCAGCUCACAUGGAAGACCAAU
CCUUAGGUGAAGAAAAUAGAUUGUCGUUUCCAAGUAAACAAUUGACCUCUUGAUCACUGU
ACUUUUUUCAUCAUUCUUUUCACUAGCAUUGCUUCUGGUCCAAGUCUCUACAGCCUCGUG
UUUCAAUUUGCUUUAUUCUUCUCUUGUUUCCCUUUUAUCUUAAUUAAGAUGGUGUCCAGG
CCAGCUUGAGCAUCUUGACAGCUCAAGUACUCCAUUGGCUACCUCCCACCAGCACAAGUA
UCAAAUAACUCCACUCUUCAAGACUUAGACAGAUGAGAAGAAGUCACCUAGCGGUUUUUU
GUCUCUGCUGGAAUUUAAACACUGGUUUCCGGUGGUUAAGUGCUUAAUUUUUCUCCUAUC
UAAAGCGCUUCACAUUUCGUCUAGUGUUUGGAAUAAAUAGGAAUACAUAUGCUCUUGAUG
UUCAGAAGUGGCUGCUUGUGAGCUGGAAACCAUGGGCUUUAAUGCAACGAGCGAGCUAUG
UCUAAUGGCUUGCGGCUUGGCUCUCUUUGCUUUAUGUUAAAAUCGGCUGCUCAUCCAGUG
UCCUUAUUGAACCAUCGUUGCAGGCUAUGUUCUACCCUUUUUAUUCCUUGCCGUGUCUCA
UCCAAAGAAACCUACAAUCAUCAGGUUCUACGAGCAAGAACUUUACUUCAGCAGCAAGCC
CGCAAGAAACACAACCACUCAUUUAGAAUCAUGUCCUAAAAGACGCAUGUUGCAAUAUUG
UCCAUGUAUUUUGGGUUGGUUAGUUAUCUAUCCUUUCUCAAUGUAAGAUCCAGACCACCA
AAAGAAUAGGAGAAAAGAUAUGUAAGAUGCAACCUUUAUCUGGAUUAAGACAAGCACUUU
AAUGGUGACAGAUGGCAGAAAAACAAUAGGUGAAUAAAUUUUGCAAUCACAUCCAGGAAA
UAUUAGAAAGAAUCCAAUAACCAUUUGUCGAGUGUGUGGGACAAUUCUAUAAUAUUAUAA
AAGAUCAGGCCUAACGUGCUAGGCUUAAUAAAGGGCAAAAAAUUACUGUUCAAUGCACUU
CAUCCAAAUUCCUUGACUCAAUCUUGAGGUGGUGGAAUUAUUCUCUGGGACAAAAAUAUU
AAAAACGGAACUGCUAGGUGAAUGAUGGAACCAUAUGCUAGAAUUAUCAAAGAUGACAAA
GUUUUUCACCAUGUAAAAGGCAUACAUGGCCAAAGGAAAAAGGAAAAGAUGGAUGGCAAC
UCGAGUAGAUGGCACUCAUGCACCAAGACAAAUGGCAUAGUCCACAAUCUAGGUCGGACA
UAAAGUAUGGAAAACCAAAUAAACAAGUAAAAAUAAGAAGUCGGUGCAGUCCUUGAGUCA
CUUUUUCUUUUUCUAUCCAGUCAUGUAUGUCAUAUUAUCAGAUGGCUUGUCCUUCCCAAU
AUCUCAUAAGUAUUUGCAUGUUUUGUGGUCUUUGGUUCUAUGGGAAUUGGUCUUAGUUAU
ACUUCUGUCAUAGUUACCGGAAAGUUCAUUUCACGAGUUUGAAAUAUGUCGUGCUGAAAA
AAAGAAGUUUGAAACACAGUAAUGACUGCCUCACAUCAGAGCAGAACUAUAUUUCACAUG
AAUAAGGAGAAUUUCGAGACAAGAACUUCAGGGCCAAUAGUAUAAUAAAAAAGUUGAAAG
UUAUGCAUCAUGAGUACGACCGCAUUUAUGAGAAUCCACACAAGUCAACCUAAUACAACU
UUUUUAAAAGAGACUACCAAGCAACUCGAGACUGCAUAUGUGAUAUGUCCACCUUCCAAG
ACUACAACACAUUCUAUUGGAAACACUUACAAGAAACUGCUGCAACACAAACUCUACAGG
AGGAACAUCAACACAAGCAAUGAUUUGCGUCAAAACAAUGAUUAGUGGUAAUGAUAACUU
ACCAACAAUAUUGCCACACUAGAAUGAAUCAAUAAUAUUCAAUGUGACAAGAAGAGGUGA
AAAUGGAUUAUGGAUGGAAUGGUAAGUGAUCAUGAACUUAAGUAUUCUUCCCAAUUUUUG
UUUCAUAAACCUGAUAGGUUUGCUUGCCACCAACCAUGGUUGUGCAAGUCAAUAUUGUAA
UAGCUGCUCCGCUAACUAUUAUUCUAGAACUUAAGCUGCAAACAAUGUAAGAUGAUACUG
UAUUUUCUAUCAAAAGAAGUUCCCAUCAUCAAUAAAUUAAUAACCUUCCCUGCACAUCAC
CUAAACCAGCCUAUUAGAAGUUAUCUUUUAUUAUCACCUUGCAUGUUUUCAUGUGGAAGG
UUUUUUUUUU

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 [-679.50] kcal/mol.

2. The frequency of mfe structure in ensemble 9.77637e-37.

3. The ensemble diversity 728.49.

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