lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-484.20) is given below.

1. Sequence-
CGUAGAGCACUGUCUAUAUUGGCAUGUGGCGUUGGUAUAGCGAAAAGAUAUUGGAUUGGA
CAACAAUGUGACAAGUUUUUGGAGUUCUAACACUUUCAUAACAUCAAUGAUUUGGAAGAA
CUGUGUAUACUAUAGAUCCUGCAAACGGAUUUCCAUUAAUUAGCACACGAACUAUUAACA
AUCUACCAGCAGACUGUCUUUUUGCAUUUUACUUCAUUAUUAUUCUUUAUCCCAUAGAAG
UGGAAUAAACAAGAGAACCAAUCGUCAGAAGCUUCUGAAUGAGACUGCUGCAUUGAGCUG
AAUUUCGCUACGAUUAACUUUUGAUAUUUUAUUCCUAUUACUCAAAGCGUACAACAAUCU
AACUCUAGAACAGUUACAAAUUUCUUCUUAUAAGGCCUUUGUGCAAGGUUGUCCUACCUU
GAGCAUUUCCUCAUCAACCAGACCUCGAUCUUCAUCAAAUUUGCAGCACACGCAAUCACA
CCUCAGCAAUAUAGCUAUCAUUAAGCUCCACGUCAUCACACCUCAGCAAUAGAGUACAGU
GUAACCAAGAAAGAAGGAAAAGAUUUUGUUAUGAAGAACACAAUUCCGCAUCGGCGGAGG
AAUGCCCAAAAAAUACACUUGCUAUGCCUAAAACUUACAAUCAGAAACAUGCAAUAUGAC
AUAAAGGACCUGCUUGGGAUUUCGAUCACAACCUACACCGGUGACUGUAGAAAUAGGCAG
UUCAAUCCAAAAGAGUCAAUCUUUUAGACAGAAUCAGCUGAGAAUUUUGUUUCACAUUCA
GAUCCAAAUUUGGAAACUACUUAUCCAUAAUCCUUGUUUUUAUUGUUUAUUAAUGUUCCA
UGAUCCUUUUGACGGCUAAUUAAAUCAAAUACAGUUCCAGUAACUAGUUUCAACCACCAA
UGAAAGAUGAAACUAAGAACUUGUUCGAAGAGUGUUGAAAUCACAACUAAUUUUAUGGCU
CAUGCCAACCAGGAUAGAUCACAAACAGCAGGAACAGGUAUCAACCUAAUUUAAAUCAAU
CACUUUCUUGUUCAUACAGGAAUUUAAGGCAUCGCCACUUCAGAUUCAUCAGUAGACAUC
AAAUACAGAUACAGCAAAAUCUAUGAACACCAGUAAGCUGAAACAGAUCCACCACGCUUC
AGAAACAUGUUAAAAACCAAAACGACAAACGCACAUGUCAAACAGAUCACCGAGCCAAAU
AGCAAUCUUUUGGAGCAUGUACAGAAGCUAGAAACAUCAUAUUAGGUUCAAUUUACAAAU
CUACAAAUCCUGGAAACAGCAACAGCAGAGUGAUGUAAACAUGAUUCUGCUGAAACAAAC
CACUCCCCCACACACUUCCAUCAUGUGUUGGUUGACCCAACUGGCUUCAUACCGUCUCCC
CUCCCCAAGUCCCCCCAACAAAAGUAAACAAAGAUAUUAGAAGGAGAUGCCUGCCUUUUC
AUCAAAAGAAAUUAGGAGAAAUACUAACAGGGUUCUUCAAAAAGGCUAUAAGAAUAUUUA
UAAUUCCAAUAAUUACCAAAAAGUGGACUUUUUUGGGAAAAUGUUCCAAUAAUUCCAAGA
AGAUGGAUUUAAAGGAAAACUAAGAGUGCUCAUUUUCUUUGUUUCUGCUUUUAAGAACUG
AUAUAAACAGCACCGGUUAUUGAGACAAAUAGAAAAUGUAAGGAAAAUGGAAAACAGCAU
ACAUGUUGCUUCUUGCGACAACAUAGCAUUUCCGAGUUUCCAAUCUUCCCAAUACCACUC
CAGAUAUUACUUAAUUAACCGUGUAUACAGAAAAUUCUUAUAAAUCACUACGCAUUUAUG
AUUGGUAUCAGAUAAUUUGAUUAAAAUCAAUGACCAACAGCAAAAACAAACCCCUUUUUU
CACCAGCUAUUGAAGUAAGUAGAAAAUGCGAGCAAACACUGUACAAUUUGGAUCCUACUA
CCACACAUUUGUGUUUUUCCCAUCUUCACGUCAACAGUCCAGAAUUAUUUAUUGAAGACU
GCUACUGAUUUUAUUGAUUUUAAAACAUAACUCUAACUAAAACAAUAUACAGAGAUUUUG
UUUGCAUCGAAUAAUUUGUUUCGGAUCAGCAGUCUCUGAAAACAUCAUAAUGGGUGAAAA
UAACAUGAUAGAAGAUCUAGAAGGUCACAUUUGCCAGAUCUUCAGCAAGAUUUCCAGAUA
GGGAACAUACAAGAAACAGGAAGUACGGGUAAUAUUAGAUAACAAAACUGACAUCAAUCC
UCAAUACGCUAAUCAAAAGAUACAGUAAUGUUUGAAGUAACCUAAGAACUAACGAAAUAG
CAGCAAAUAUUAACUAACAGCCACACAUAAGAGCAGAUAGGUGAAGCAGCAACAGAUGUA
CAGCAGUCCAUGUAACGAAAGAUUUCAGAAUCUGCAAUCAGGAAAUCACCACAACCAUUA
AAAGCAUGUUGCAUCCAAGAAGCUCUCAAGACACCUCAGUAAUAUGGAGGGAUGCCCUGG
UACAUCCCACCUGGUGGAACCCUCGACCC

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 [-529.34] kcal/mol.

2. The frequency of mfe structure in ensemble 1.56361e-32.

3. The ensemble diversity 653.14.

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