A Grammar-Based Unification of Several Alignment and Folding Algorithms

Weshowin this paper that manypopular models of folding and/or alignment maybe described by a new formalism: multi-tape S-attribute grammars(MTSAG's).This formalism relieves the designer of biological modelsof implementationdetails which may hinder his inventiveness. To completethis formalism, wedesigned and implementeda tool which, given a MTSAG,will output an efficient parser for this grammar. Wealso showthat MTSAG'soffer a new, efficient and useful wayto handlestochastic context-free grammarsand tools that generate them.

• Type: Conference
• Year: 1996
• Where: ISMB
• Authors: Fabrice Lefebvre
• Keywords: Computational Biology, Efficient Parser, Handlestochastic Context-free Grammarsand, ISMB 1996, Manypopular Models