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Bellman's GAP--a language and compiler for dynamic programming in sequence analysis.
Georg Sauthoff1, Mathias Möhl, Stefan Janssen
1Center of Biotechnology and Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany.
Bioinformatics (Oxford, England)
|January 29, 2013
Summary
Bellman's GAP simplifies bioinformatics tool development using a declarative programming style. This system reduces errors and enhances modularity for dynamic programming algorithms, yielding efficient C++ code.
Area of Science:
- Bioinformatics
- Computational Biology
- Algorithm Development
Background:
- Dynamic programming is essential in bioinformatics but complex to implement.
- Developing dynamic programming algorithms is prone to errors and time-consuming.
- Bellman's GAP aims to streamline the creation of bioinformatics tools.
Purpose of the Study:
- Introduce the Bellman's GAP system and its declarative language, GAP-L.
- Demonstrate the system's ease of use and reusability in developing bioinformatics algorithms.
- Evaluate Bellman's GAP for real-world bioinformatics applications.
Main Methods:
- Algorithms are described declaratively using tree grammars and evaluation algebras.
- Declarative modules are compiled into efficient C++ code.
- Variants of common bioinformatics algorithms are developed using Bellman's GAP.
Main Results:
- Bellman's GAP facilitates the creation of error-free, modular, and easily modifiable dynamic programming algorithms.
- Generated C++ code is competitive with hand-crafted implementations.
- The system enables efficient development and reusability of bioinformatics tools.
Conclusions:
- Bellman's GAP significantly eases the development of dynamic programming-based bioinformatics tools.
- The declarative approach offers advantages in terms of correctness and maintainability.
- The system is a viable platform for implementing practical bioinformatics solutions.
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