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Open Access Highly Accessed Research article

Gene finding in novel genomes

Ian Korf

Author Affiliations

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK

BMC Bioinformatics 2004, 5:59  doi:10.1186/1471-2105-5-59

Published: 14 May 2004

Abstract

Background

Computational gene prediction continues to be an important problem, especially for genomes with little experimental data.

Results

I introduce the SNAP gene finder which has been designed to be easily adaptable to a variety of genomes. In novel genomes without an appropriate gene finder, I demonstrate that employing a foreign gene finder can produce highly inaccurate results, and that the most compatible parameters may not come from the nearest phylogenetic neighbor. I find that foreign gene finders are more usefully employed to bootstrap parameter estimation and that the resulting parameters can be highly accurate.

Conclusion

Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.