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首页> 外文期刊>Computational Biology and Bioinformatics, IEEE/ACM Transactions on >Product Grammars for Alignment and Folding
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Product Grammars for Alignment and Folding

机译：用于对齐和折叠的产品文法

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We develop a theory of algebraic operations over linear and context-free grammars that makes it possible to combine simple “atomic” grammars operating on single sequences into complex, multi-dimensional grammars. We demonstrate the utility of this framework by constructing the search spaces of complex alignment problems on multiple input sequences explicitly as algebraic expressions of very simple one-dimensional grammars. In particular, we provide a fully worked frameshift-aware, semiglobal DNA-protein alignment algorithm whose grammar is composed of products of small, atomic grammars. The compiler accompanying our theory makes it easy to experiment with the combination of multiple grammars and different operations. Composite grammars can be written out in for documentation and as a guide to implementation of dynamic programming algorithms. An embedding in Haskell as a domain-specific language makes the theory directly accessible to writing and using grammar products without the detour of an external compiler. Software and supplemental files available here: http://www.bioinf.uni-leipzig.de/Software/gramprod/
机译：我们开发了一种关于线性和无上下文语法的代数运算理论，该理论使将对单个序列进行操作的简单“原子”语法组合为复杂的多维语法成为可能。通过将多个输入序列上的复杂对齐问题的搜索空间显式构造为非常简单的一维语法的代数表达式，我们证明了该框架的实用性。特别是，我们提供了一个完全工作的可感知移码的半全局DNA-蛋白质比对算法，其语法由小的原子语法的乘积组成。伴随着我们的理论的编译器使结合多种语法和不同运算的实验变得很容易。复合语法可以写出来作为文档，并作为实现动态编程算法的指南。在Haskell中嵌入作为特定于领域的语言可使该理论可直接用于编写和使用语法产品，而无需绕开外部编译器。可在此处获得软件和补充文件：http://www.bioinf.uni-leipzig.de/Software/gramprod/

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