RNA structure and shape combinatorics
Abstract shapes were introduced by Giegerich et al in
Combinatorics of abstract shapes were recently studied in
This website allows for empirical studies of structure and shape combinatorics. It assumes you have some background in the framework of algebraic dynamic programming, which is used to implement these analyses. The website provides
Modes of OperationWhile each evaluation algebra serves a meaningful purpose by itself (see algebra explanation), the fun comes from using products of algebras. You can use up to three algebras in a product here, although theoretically, there is no limit. Note that the product is associative.
Simply speaking, a product algebra A *** B first evaluates the folding space of a sequence under algebra A, and thereafter, the candidates returned by A are evaluated under Algebra B. The product A *** B is always defined, but does not always satisfy Bellman's Principle of Optimality. If a product algebra returns something that looks weird, please check the formal definition of products in