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A folding algorithm for extended RNA secondary structures.

Höner zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL - Bioinformatics (2011)

Bottom Line: Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment.We accompany this model with a number of programs for parameter optimization and structure prediction.All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/.

View Article: PubMed Central - PubMed

Affiliation: Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria. choener@tbi.inivie.ac.at

ABSTRACT

Motivation: RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment.

Results: We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction.

Availability: All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/.

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Prediction of non-canonical base pairs with RNAwolf. (A) Known structure of PDB entry 1dul. (B) Constrained prediction (canonical base pairs were given) of 1dul. Only the central part of the structure is shown. The outer part of the stem contains only canonical base pairs and is not shown.
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Figure 6: Prediction of non-canonical base pairs with RNAwolf. (A) Known structure of PDB entry 1dul. (B) Constrained prediction (canonical base pairs were given) of 1dul. Only the central part of the structure is shown. The outer part of the stem contains only canonical base pairs and is not shown.

Mentions: A constrained folding variant of the ‘enhanced-Nussinov’ algorithm can be used, for example, to predict non-canonical base pairs in large interior loops of structures. As an example, Figure 6, shows that RNAwolf is able to correctly predict the non-canonical base pairs in a situation where the canonical base pairs are already given, i.e. where the input consists of both the sequence and a dot-bracket string representing canonical Watson–Crick base pairs. Only the zig-zag motif (upper part of the interior loop) was not predicted, presumably due to the large penalty of +3.89 for each of the two 1×2 stacks.Fig. 6.


A folding algorithm for extended RNA secondary structures.

Höner zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL - Bioinformatics (2011)

Prediction of non-canonical base pairs with RNAwolf. (A) Known structure of PDB entry 1dul. (B) Constrained prediction (canonical base pairs were given) of 1dul. Only the central part of the structure is shown. The outer part of the stem contains only canonical base pairs and is not shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3117358&req=5

Figure 6: Prediction of non-canonical base pairs with RNAwolf. (A) Known structure of PDB entry 1dul. (B) Constrained prediction (canonical base pairs were given) of 1dul. Only the central part of the structure is shown. The outer part of the stem contains only canonical base pairs and is not shown.
Mentions: A constrained folding variant of the ‘enhanced-Nussinov’ algorithm can be used, for example, to predict non-canonical base pairs in large interior loops of structures. As an example, Figure 6, shows that RNAwolf is able to correctly predict the non-canonical base pairs in a situation where the canonical base pairs are already given, i.e. where the input consists of both the sequence and a dot-bracket string representing canonical Watson–Crick base pairs. Only the zig-zag motif (upper part of the interior loop) was not predicted, presumably due to the large penalty of +3.89 for each of the two 1×2 stacks.Fig. 6.

Bottom Line: Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment.We accompany this model with a number of programs for parameter optimization and structure prediction.All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/.

View Article: PubMed Central - PubMed

Affiliation: Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria. choener@tbi.inivie.ac.at

ABSTRACT

Motivation: RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment.

Results: We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction.

Availability: All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/.

Show MeSH