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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/.

Show MeSH
Decomposition of one non-terminal in the full loop-based model with triples. The l.h.s. of the production rule denotes a structure enclosed by a base pair where the base at the 3′ end is part of a triple. The second base pair of this triple ends within the structure. The structural element is either bulge like (first column) or multiloop like. In the first case, we have to distinguish whether the enclosed structure has a normal pair or a triple at its 5′ side. In the multiloop case, we use the linear decomposition into components familiar from the Turner model with a non-terminal denoting a partial multiloop containing at least one base pair. Here, we need to distinguish whether the 5′ end of the rightmost component and 3′end of the left components are triples or not. As the multiloop part is not implemented in our current version, it is grayed out.
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Figure 4: Decomposition of one non-terminal in the full loop-based model with triples. The l.h.s. of the production rule denotes a structure enclosed by a base pair where the base at the 3′ end is part of a triple. The second base pair of this triple ends within the structure. The structural element is either bulge like (first column) or multiloop like. In the first case, we have to distinguish whether the enclosed structure has a normal pair or a triple at its 5′ side. In the multiloop case, we use the linear decomposition into components familiar from the Turner model with a non-terminal denoting a partial multiloop containing at least one base pair. Here, we need to distinguish whether the 5′ end of the rightmost component and 3′end of the left components are triples or not. As the multiloop part is not implemented in our current version, it is grayed out.

Mentions: The grammar of Figure 3 can be extended to incorporate the standard loop-based Turner energy model (Turner and Mathews, 2010) (which distinguishes hairpin loops, stacks of two base pairs, bulges, interior loops and multibranched loops). The modification of the grammar is tedious but rather straightforward, as seen in Figure 4. Instead of treating the base pairs themselves as terminal symbols (as in Fig. 3), this role is taken over by entire loops. Note that as in the case of ordinary secondary structures, each loop in a given structure is uniquely determined by its closing pair. The energy contributions now depend, in a more complex way, on the characteristics of the loop, hence we also need additional non-terminals to describe e.g. the components of multiloops.Fig. 4.


A folding algorithm for extended RNA secondary structures.

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

Decomposition of one non-terminal in the full loop-based model with triples. The l.h.s. of the production rule denotes a structure enclosed by a base pair where the base at the 3′ end is part of a triple. The second base pair of this triple ends within the structure. The structural element is either bulge like (first column) or multiloop like. In the first case, we have to distinguish whether the enclosed structure has a normal pair or a triple at its 5′ side. In the multiloop case, we use the linear decomposition into components familiar from the Turner model with a non-terminal denoting a partial multiloop containing at least one base pair. Here, we need to distinguish whether the 5′ end of the rightmost component and 3′end of the left components are triples or not. As the multiloop part is not implemented in our current version, it is grayed out.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: Decomposition of one non-terminal in the full loop-based model with triples. The l.h.s. of the production rule denotes a structure enclosed by a base pair where the base at the 3′ end is part of a triple. The second base pair of this triple ends within the structure. The structural element is either bulge like (first column) or multiloop like. In the first case, we have to distinguish whether the enclosed structure has a normal pair or a triple at its 5′ side. In the multiloop case, we use the linear decomposition into components familiar from the Turner model with a non-terminal denoting a partial multiloop containing at least one base pair. Here, we need to distinguish whether the 5′ end of the rightmost component and 3′end of the left components are triples or not. As the multiloop part is not implemented in our current version, it is grayed out.
Mentions: The grammar of Figure 3 can be extended to incorporate the standard loop-based Turner energy model (Turner and Mathews, 2010) (which distinguishes hairpin loops, stacks of two base pairs, bulges, interior loops and multibranched loops). The modification of the grammar is tedious but rather straightforward, as seen in Figure 4. Instead of treating the base pairs themselves as terminal symbols (as in Fig. 3), this role is taken over by entire loops. Note that as in the case of ordinary secondary structures, each loop in a given structure is uniquely determined by its closing pair. The energy contributions now depend, in a more complex way, on the characteristics of the loop, hence we also need additional non-terminals to describe e.g. the components of multiloops.Fig. 4.

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