lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-404.00) is given below.

1. Sequence-
CGCACAUAAAUUUCCCUCCAUAUGCUCCAAUAUUAUUAUACACGUCAAUAUUAUUUGUAG
AAUAGUCAUUACAGAUCCAAAUAAGAAACUAAAAACAUGAUAGAUAACCCCAAUCCCAGC
AACUCUUCUAUUUACUCCGGCCAAAACUUUUCACCGAAAACCUGUCAAAAUAACCAAAAA
AAAAAAAAAAAAAAAAAUCUAGACCCGAACACUAACAACCAAAUAAAUAGAACAUCUAAA
GGCUAGGUGACAGAUUCCUAUAAGCAUGUUCUCUACUAGAAAUAUAAUACAAACAGAAGC
ACAUUGUCAUUGAGCGAAAAAUAUGAAACAAACCACACAAGAAUUGCAAGAACAUACCUG
GAUGUUUUUCAAUGAGCACGCAGACUAGCAAAAACGAUAUUUAGAACACUUCGAUAGAAC
ACGAUCCGGUUAAAGCAGAGACAGAUAAAACAACAAAUCAUAGAGGAAGCAGUAGCAGAG
UAAGAAAAAUCAGAGAAGCCAAAGUCAAAUAUUGUAAAAGGCAAGAGCUAGAUGUGUGUA
UAUAUAUAUAUAUUUUCUUUUUGUUUUUUCAGAGACUUAGAAUGCGAAAAGUUUAUGAAC
AAAAGUAAUUGAAUAAGAUAUGAUUAAGUGAGGGUGAAGAGUAUGAGAUGAAAAGUGAUU
UGAAAAGUGAACGGUGAAUGGUGAUGUUGUGUAGCGUGAAGCAGAGAGAUUAUGAGAUGA
UUACAAAAGCAUGCAAAGGUUUGUUUAUAUAGUGAGGGGUCCAAAUUGAAAAGGAAGAGC
AAAUAUUCAGCAUAAUCAAUUUAAGAGAUAUCUUCUCUAAUCAUGGGUUAACUCAAUCAA
CAGCACAAGGAAAAUAAAUAUCCAGUUAGAAGAGAAAAGAACAGGGAAGUAUAUCUAAGA
AUCAAUCAAAGAAGCACUUUCCUUAUUUAAAGCCAACUCAGACAAUCAAGUGACAGUAGA
CAGGUCAAUUUUUACCAUAAUAAAUAAGUAAUAAUAUAUCAUAACCAAUUAUUCACAUAA
UCACAGAGACCAUUCAAAAUAAAUCAAUCUAGAGAAGCUCUUUCUUUUAUCAAAUGGGUA
GAAUCGAUUUCAGAUAGAAAUUCUACGAGUUACCAAAAACCUCAAAAUCUGUCCAAGUAA
GACUUGGGAGGAAGAAAAAAAAAUCAAAUCAAUCUAGUUAUCCCACAGAAAGCAAUCAGC
CCUAAUAACUAUUUGCUAAUAAUAUAUAAACAACAUAAAUUAGAGUCAUCACAACUUUAU
AAGAUUUUCAAAGAACAGGCUAAGGAUGAACAGUAUUGCGCAAAUUCCAUGAAAUGACCC
GGUGACAUGACCAAGAUUUUGUCCAAAAUAAAAUAAUUAUCAGUCAACAGUAAAGAAGAA
UAACAACAAUAUCAGCCAAUUAAAAAACAAACUAGUACCCAAGUUAGAGAAUAAGGGUUG
AAUCACAAGUUCAUAAAGUUAAGCAUUUUGAAAUAUAAUAAUCCAAGCACUUUAACAAAC
AUGACAUUCAAGAUAUUUAAACCAAAACACAAACCUUAAGACGGAUUCUCAAGAUAAAUU
UAAUAUUUUUCAGGUACGACUUUGACCGGAGAAGAAGAGCAAUGAAUCGCUGCUGGACUG
AUGGAGGCAACAUCGGCGUUGAGGCGGUGCUAUAGAUGAGAAUAAAGCAUUCCUGGUUUC
UCCCCGGCACUUUACCGGACAGUGGUGACAAUUGAGUUGAAAAGGGUGGCGUUGCAUCAC
UUAUGGGGUCUUCAUCGCGGAUGUGGCGUGGUUGAUGAUGGUCAAAUCUGCAUAGCCAUU
AACAGAGAUGGGGAAGACGCCGUUGAUGGUGGGGUUUCAUGCACGGUGGAGGUGCUGCCG
UGGCGAAUGAACCUUGACCGGCGAACAUUGGGGUUGAUGGAGGUGAUCGCUGGUCGGAGA
CGAUGAGACAGACAAAGAGGAUGAAACAAGAAAGUUCAACAGCGAUCAUGGGACUCGCAG
GCGGUGAAGGAGAACAGGCGGCGUGGGAGUCGUGUGGAGGAGAAAAGUGUUUUAGAGAGA
GAAGGGAUAGAGAGAAACAGUUUAGAGGCGGCUGAGUUGUUGA

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 [-442.32] kcal/mol.

2. The frequency of mfe structure in ensemble 9.95062e-28.

3. The ensemble diversity 495.26.

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