ArticleBioinformatics (Oxford, England)2013
Bellman's GAP--a language and compiler for dynamic programming in sequence analysis.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Infrared: a declarative tree decomposition-powered framework for bioinformatics.Algorithms for molecular biology : AMB · 2024Article
- Simulation of Folding Kinetics for Aligned RNAs.Genes · 2021Article
- Ambivalent covariance models.BMC bioinformatics · 2015Article
- The RNA shapes studio.Bioinformatics (Oxford, England) · 2015Article
- Thermodynamic matchers for the construction of the cuckoo RNA family.RNA biology · 2015Article
- Pareto optimization in algebraic dynamic programming.Algorithms for molecular biology : AMB · 2015Article
- Analysing RNA-kinetics based on folding space abstraction.BMC bioinformatics · 2014Article
- Riboregulation in plant-associated α-proteobacteria.RNA biology · 2014Review
- The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective.RNA biology · 2013Article
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Authors and funding
4 authors.
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Abstract
motivationDynamic programming is ubiquitous in bioinformatics. Developing and implementing non-trivial dynamic programming algorithms is often error prone and tedious. Bellman's GAP is a new programming system, designed to ease the development of bioinformatics tools based on the dynamic programming technique.
resultsIn Bellman's GAP, dynamic programming algorithms are described in a declarative style by tree grammars, evaluation algebras and products formed thereof. This bypasses the design of explicit dynamic programming recurrences and yields programs that are free of subscript errors, modular and easy to modify. The declarative modules are compiled into C++ code that is competitive to carefully hand-crafted implementations. This article introduces the Bellman's GAP system and its language, GAP-L. It then demonstrates the ease of development and the degree of re-use by creating variants of two common bioinformatics algorithms. Finally, it evaluates Bellman's GAP as an implementation platform of 'real-world' bioinformatics tools. AVAILABILITY: Bellman's GAP is available under GPL license from http://bibiserv.cebitec.uni-bielefeld.de/bellmansgap. This Web site includes a repository of re-usable modules for RNA folding based on thermodynamics.
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