lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-276.60) is given below.

1. Sequence-
AAGCCAUGCAGAUUCUGCCAACCCCCCAAACGUUCCAGAUUGAUUGGAAUUGCAGAAGCU
GAAGAUUUGGUGAGUCCUCGAGGACCGAGCUUUUAAAUUUUAUUUUAUUCUUUCAUUAUU
UAGAGUUGAGAUUUUAGAGUUAUUUUAUUUUAUCUUGAAACUAGCAGGCUUUCGAACAAG
AGUAUUGAGUAGAGUUAAGACUUGCAGUUUUCAUAUCUAUUGCAGUAUUUAUUUUUCAUU
CUUGUGAGGUGCCUAUUACUUUAUAUUGUUACUGAUAUUGCUUUCAAUGAGUAUGAGUGU
AUAGUUAUACAUGAGACAAGGGUUCAUGCAAGGCUACCUAGUCGCUAAGGAUGUCGUAAC
GUGCCCAAGGGGUUAGCUCGGUUCGUGACAAACCUACUCUGAUCCUCCAGGUUCCCUGUA
UCAGGAAAACAAAAAGUGCAAAAAUCUCAUCUCAAUAGGUGCCUUACUGUUGUUUCCAUC
UUAAGCAUCUACACCUCCCAACAAAGUAAAUCUUCUGGAAUGUCCUCUCCCUAAGACCGA
GUUAAGUCCAUGACCGCGGGAAGAGUUAACCACAUAUAAGAGGUAGCUAAUUAAUUGAUA
GCACUCUGUUAAUUUCUUUAUUAGUUUGAGGUAUGUUUCUUUCUGUCCUUUUAAAUAUCU
UUUUAGUUUGAGGUGUGUUCUUCCUGUCUUUUUCUAUAUUCUCAAGCAAUGCCUUCAAGU
AUUUUGAGGUACAACCUCUAAUAGUAUACAUUUGCAGGAUGCUCCUUUUAAAGUGAUGGA
CGAUUACAGAAGCUUGGGGCACAGGUAUUAAAAGACGGCUUUCAUAAUAAAUAAGACAAG
CGAUCAAGCUGGCAAGUCAGGGAUAGAGGAUGGAUUUCUUCCCUGCAUUCCUUCCUUUCA
AAAAAAGUAAAAACGUUUGGGCUGCUUUCCCAUAAAUUGAAUUGUAGAUUUCAAAUGAGG
GAGAUGGAUGAAGGGAAAAAAAACUGGCAUCAACUUUAGAAAGAGGUGUUUAGCUCCCCA
ACAGUGAAAGUGUAGAUAAUUGUAACUAGGACACACUGAUGCAGAACCUAAUUUUUAUAU
GUUGCUACGAUAGCAUAUGUAAUAUUUUUGGAGACACUUCAUUACUAAGAAAAAUAUUUA
GUUAACUAAUUAGGAGAACAUAUUGGACCUGUGCAUAGCUAAACUUCACUCAUAAUACAU
AAUACGGGG

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 [-299.48] kcal/mol.

2. The frequency of mfe structure in ensemble 7.49128e-17.

3. The ensemble diversity 311.60.

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