lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-395.40) is given below.

1. Sequence-
CCUACAUUUAGAUACUGUCGUCAUUUGCUUGUAUUACAUCCCAAAUCUUAGGCAAGACAU
UGCGUCUAAAUGUUUGUAUUUACAAAUACUAGAUUAAUACAUCAAAAGAAAAUUUUAAAA
AAAAAAUACAAAAGAUCAAGGAUCCAUCAUCGCCCUACGAAACAACUGGAUCAUACAAAG
GCAAUUUACAGCCACUGUUGUAGCUCCAGUCAAGAAUCAAGACAAUCAACCACCUAGAGC
AAGUUCCAAACCUAUGUACCCUCAAACAUGGGAAGGGUUGGCUAAAGAAACUGCACGGGG
CAAGGAUGGAAGAGAAGUAACAGGGCAAAUUAUACAGUUCUCUAUAUUCUAGAAACCAGA
GCAACUUCUAACUUGGCAUAAUUAGUUGUAGGAAAUCAACAUGCCCUACUAAGCUUAACU
UGGCGCAAGUACUUGCAAACGAUCAACUUCUCAUACCUCAUGAUUUGAUGUCUGUAAAAA
UAACCUCUCAUAUCACUAACCACUUUUUUUCAAAACACAGCCACCCCACCACACUCGGUA
GGAACAAAUAAUGGAGCAUUCAUAAGAGGAGCAGUAUUGAAAGGCAUCAGCAAAAUAAAU
ACAAAACAAAGAAGAGAUGGCUGACUUCAGAUUGGAGCAGCAGAUCUUGAAACAACAUUC
UCAUCAAACCAACGCAUAAAAUACGAAUACCUAUUUUUGAAUAUACGAGUAAAUUCCACC
AAACAUGCUGCUGAUUCUAUGCAAUAAAUAACAGGAGCUUGCAGAUGAAUCAUAUAAAAA
AAUGUUCUUUUAGUUUGAUAGGUAAUCUUAUAACAAAAUUAAGCAAGUUAUAAUACGAAU
AUGAGACUUACCAUAAGAUUUUUACCUGCUUCAAUUAAUUCCAACCAGUACUCCCAAAAA
GCUAUCGGAUUCCACAGUGAAGCAGUGAAAAUUAUAUCACUGCAAUUUGACAAACAGAUA
CAUCUUGCACUACUAAACCACACAGAUAACUGCAUUGAAGAUCCAGUGUCUACAAAGAAC
UUACGCACCCUUGUAGCUUAAGAUGUACGUACAUUCCAUAGCCACUACAUCCUUCUUCAG
AAGAGCGAUCUACUUCUCGCAAGAACUUUUUCCAAUUAAAUGACAAGGAUAUUCAGAAAA
UCACGGUUGAAUAUCAUAAGCAGAUAAUAAAGAAACAUGUGGGAUUUCUAGUAACAUAGA
UCUUUUGAAAGGGCUAGUAUCCCAACAUUGCAUCAUAACAAACUAGAAAAACACUAGGAA
AUCCGCACCAGGUGUCUAGCAUCUAGAGCAUCAAAUAGGCAAGUGCAACUACCAGUAGAU
UCAUACAAAUAACAAUAAACCAAUAAAAAAGACAUCAGGACACAUUGCCGAGAUUUAAGA
GUUGAAUUCAUCUAUAGUACAACUACAUAAGGGAAGAAAGGAUGAGGCCGCUGGCUACAC
AGGUUCUUGGAUGCACAAGAUUGGAAGUAUAUGGUGUCAGGGCUGGCAAAUUUCGAUAGU
AGGUAAGAUCUUCGGAUAUGGUCCUGCUAAGGAAAACAUCAAGGUAGGCAAUGAUUUUCG
AUGUCUGCAUUCAUCUGGUCAUCUGGUUUAGGCAUGAGGCUUCAUCAAAGGUGACAGUAG
CCAGGCUUCAGGCUUCAGAUAUCUCGGCUGUUUAUAGCGAGAGAAAGGAAACAAAGGGAA
AAGAAUACCAUUAGCUUCAUAAUUGGAAAACAGGUUAGGUCAUCAUACCAAAAUGUCUAG
AAUUUUGCACAAGUGGGGCUAAGUAUAUAAAACCAGCAAAUUAAAUGAAAAAUACAAUGC
AAUAGAACCAUAAUUCAUGAGCUACCUGUGGUCCUGUUACAAGCACUAGUAACCAUAACU
UUUUCUCCGGGAAGCAGAAUUUUGCCUUGAUGACC

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 [-429.03] kcal/mol.

2. The frequency of mfe structure in ensemble 2.00317e-24.

3. The ensemble diversity 518.63.

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