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Dynamic programming for gene finders

Part 4. Bioinformatics

4.2. Gene Finding and Gene Structure

Basic Techniques and Approaches

  1. William H. Majoros

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g402412

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

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.

Author Information

  1. The Institute for Genomic Research, Rockville, MD, USA

Publication History

  1. Published Online: 15 APR 2005

Abstract

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.

Keywords:

  • dynamic programming;
  • memoization;
  • trace back;
  • recurrence;
  • matrix;
  • Markov model