Dynamic programming for gene finders
Part 4. Bioinformatics
4.2. Gene Finding and Gene Structure
Basic Techniques and Approaches
Published Online: 15 APR 2005
Copyright © 2005 John Wiley & Sons, Ltd
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
How to Cite
Majoros, W. H. 2005. Dynamic programming for gene finders. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.2:26.
- Published Online: 15 APR 2005
Dynamic programming (DP) is a common algorithmic technique for the efficient evaluation of recurrence relations. Owing to the combinatorial nature of the gene prediction problem and the resulting recursive formulations that are typically adopted for modeling gene structure, the effective use of dynamic programming is particularly crucial to the implementation of a successful gene finder. This article considers the major complicating aspects of the technique, such as banding, numerical underflow, memory management, validation, and the use of heuristics to achieve an acceptable space/time trade-off.
- dynamic programming;
- trace back;
- Markov model