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Gene structure prediction by genomic sequence alignment

Part 4. Bioinformatics

4.2. Gene Finding and Gene Structure

Basic Techniques and Approaches

  1. Burkhard Morgenstern

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g402413

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Morgenstern, B. 2005. Gene structure prediction by genomic sequence alignment. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.2:27.

Author Information

  1. University of Göttingen, Göttingen, Germany

Publication History

  1. Published Online: 15 APR 2005

Abstract

Traditional gene-finding programs are based on stochastical approaches such as hidden Markov models (HMM) describing the statistical composition of coding and noncoding regions for a given organism. Comparative gene prediction, by contrast, is based on the phylogenetic footprinting principle. During evolution, functionally important sites in the genome tend to be more conserved than nonfunctional regions. Thus, local sequence conservation usually indicates biological functionality. Comparative gene-finding approaches start with an alignment of evolutionary related genomic sequences and try to identify splice signals in areas of local sequence conservation. This way, putative exons are identified that are used to construct gene models. In this chapter, the comparative genefinder AGenDA is described. Its performance is compared to more traditional approaches, and possible future developments are discussed.

Keywords:

  • gene prediction;
  • phylogenetic footprinting;
  • alignment;
  • genome annotation;
  • cross-species sequence comparison