Figure 3 - uploaded by Raphael Reitzig
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A secondary structure and the corresponding Motzkin word.
Source publication
Dowell and Eddy (2004) presented several context free grammars for RNA secondary structure prediction. Some of them are claimed to be unambiguous with respect to secondary structures. Although this property is crucial for the correctness of prediction algorithms using those grammars, it is only shown empirically, but
not formally proven. This gap i...
Contexts in source publication
Context 1
... can see two typical patterns highlighted: a chain of paired nu- cleotides, called stem (or stack ), and a little hairpin loop at its end. Figure 3 contains a secondary structure with a multi-branched loop in its center. Biolo- gists often consider further patterns, such as bulges or interior loops, but those as well as hairpin loops are only special cases of the multi loop. ...
Context 2
... is to say that a molecule is a con- catenation of symbols from Σ. Secondary structures, on the other hand, can not be represented as easily. Since sketches as seen in Figure 3 are unhandy and hard to grasp formally, many authors use a convenient string notation for secondary structures (e.g. [Neb01]) that goes by the name Motzkin words. ...
Context 3
... |||| corresponds to a linear chain of four bases whereas ((|||)) represents a stem of length two with a hairpin loop containing three bases attached. See Figure 3 for a more sophis- ticated example. It turns out that not all Motzkin words describe structures that are physically feasible. ...
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