lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-509.22) is given below.

1. Sequence-
CAAAGAUAUAACCAACAUAUAACUAAUGCAACCUUAAUUUAAAGAUUCUAGGACUAGUCU
UAUUAAGCUACUAUUAGCAAUACACCUAUUAACCAGAAAGUAGAAGCAUAUUAAUCCGAA
GCAACAAUUCCUAGUUAUGAAUUCAGAUUAAGCAACCACUGAUAAGGUGAGAAGGAUAAU
UAAAAACACAGAGGACUAGUCAUGUUAAGCAAACUAGGACAGACUUAUAUAAUUCUUUCG
AUUCAUUACAGCACACCAUAAUAAGCAAACUAACCAACUUCUUCAAAUGGAACCUAGACA
UGCUCAUACACAGUUUUGCAUCAAGAAAAUAAUUUUGUCGACUUACCAAAUAGACAUGCU
GCCACUGCUAAUUUAAACUAGUUUCUAGGGUCAUUUCACCAAAUCUUGGUUACUCGGGGA
AUUCCUAGCCAGUUUAAUAUAUUACUUUAAGUGAAGAAAGGGCUAUCAAAGAGUUAUACA
UAUUAUAAGGCAUCCAAAUUUAUCCUUGGUCAUAAUUCAGAUCAAGCAGUUACAGGUGUA
GCAUAGAACAUUACUUUAAGCCAUACAAAACUGGUCCUGCUAGCAACAGCAACUGAACUA
GCCUCUAAAGUCAUUUUAUUGUUCACAGUAUUUAAAAUGCAAGCCGACAGGUUAUACUGA
AAUAGAGUCUAGACAUACUGCUAUCAUUCAAGAAAGAGGCAGUCAUUUUACCGGGGAUAA
UGCAAACAUGAUUGUCAAGGCAUAAACAUGAUUGUCAAGGCAUCAAUGUGACACUUUCAG
GCAGUCAGUCUUCUUUCCUAUCACAUUACUCAAGCUAAACUUUCAAAUCAGGGCUGGUCA
AUAUUCACACAUUGCAUUUCCAUUUAAACACACUUUAAGACCAGAUACUCAGGUUUGAAG
AUGAAUUUUGGGGAUAAAACAAUAAGACAGGUCAAGAUUCAAACAGAGAUGCAACAUAUU
UCAAACAGGUAAUCAGCAUUUGCAGGAAGUGAAGAAAACUACAAAUUUAAUUCUUUUACA
UUCUGCCCAAGUCAGAUGAGUAAUCUGAUCUUUCACAAAAGAACAUUUAUACUUAAACUG
GUCAGUUAUUUAUUCUAUUUCACUUGAAAUAGUCCAAGAGGUAGCUAACAAAUCCCAAAG
AUUUAGAUUAGUAUUCACCCCUAUUUCACCUGUUCAUAUUGUCAAUUUGCCAAGAAAGAA
UACAAGAUUAUACAGUUCAGAGUUUCUUUCAGUAAAAUAUAAUAACACAUAGCCCAUUUA
GAAUCAUGCUAGCAUGCUUUGAAUUUUAACCACCAAUUCAUACAUGACAAUAAAAAGAGA
AAGAAAAAGAAAUCAGAGCAAUUCAUUAGUCGGUUACUAAUGAUGUUCAACUUAGCCAGA
UUUUCAUGAAAUAAACAAGACCCAAACAAGGUAGGGGGCAAACCAAGUCAAAUGAGCAAA
UAAACCGAUAAGACAAACAAUAACCUCCUCUAGAUAGAUCAUGGGACAGUUGAAAAUAAC
CAACUAUCUCAUGACUUAUUACUAGCAAACCAGACAUAUAAAAAGGCAUUGACUGAAAAU
UCUCUUCAAAAUUUAGAGAUGAUAAAGUCUCAAACAACUCCUUUUUAUAGGAAAUUAGCC
UAUUCCUUGCCGGAGACAUGCUGGACAGAUUGUAAAUCUUACAACAAAUGACAAGUUAAA
UAGAUUUCAAGCAAAACAUCAUACCCAGAAGUCAGAUCUUCUGAUCAGAACCGAGACAAG
AAGAUUCACAAACCACCAAUCUUGUUCAGGCAUCAUAGGUUUAAUGUAAAGAAAGCAUCC
UCACAAUCACGGAUUCUUACUUCACGAAGUAAAUUAACUAGUUGCCAAAGGUACUACAAG
AAAAUGACUUCUAUUUUAAAAUACCUGGAGUCUUAGAUUUUUCUAAUGUUUUACGCUAGC
AGUAAUCAAAUCAAGAUGCUUGCCAGAUUACUCGCAAGAAUAACAACAAAGAAAAUCCAA
GUAUCUCAAUGCUUGUUCAAACAAGUUAGUUCAAAACCAUGAUUGCACGAAGAAUUCAGA
CCCCAAAUACCUUCCCAUGUUUAUGCAUAGAUCAAACGACAAUUCUCAUAAAAAUGUUAA
UAUGUUUGACUCUAAUUCUUACUGUUUGGAUAUAACUCAAAUUCAUUAAUUAAAGCAAAC
UAGCAUAGUUCAAUAAACCAUAUCCAAUUGUAGACUUCUACUAAUGCCAUAAGAAAACAA
ACAAUGCAAGGUUGAACACUUAUGAGGCUGAUGUUUAGAACACAUCUAAAUUCCAACCUA
AUUUACUUACAAGAUAGAAACCAACUGGACAGGGAAAAUAAAUGAGGCAAGGAUUAUCUG
GUUAAAACUUAAGAUGUCAUUUUCAAUUCACGAUGUGAAGAUUUAAGGAAAUGCAUUUAU
CACUCAGACGAGCUAGCAAGAAAUCUGCCAGUGAAGGUUCAAACGGCUUCAAUUUACAUU
UGUAUUAAGAAACCAAGCAAAGUUUCAAAAAAUUUCAAUUCCCAGACCGAUCAAUCAAGU
AACAGGGGAAAGAAAAUAAAAGAGAAUGCUGUCAAGCAUUAGGCCAGGUUAAUAAUGGAA
CUUUGUAAAUAACUAAACAAAUUCAAAGAUUUCCUGGGGAAUGAAUAUCCUUAAG

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 [-553.45] kcal/mol.

2. The frequency of mfe structure in ensemble 6.83462e-32.

3. The ensemble diversity 661.44.

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