Gene structure prediction by genomic sequence alignment
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
Morgenstern, B. 2005. Gene structure prediction by genomic sequence alignment. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics.
- Published Online: 15 APR 2005
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.
- gene prediction;
- phylogenetic footprinting;
- genome annotation;
- cross-species sequence comparison