Gene finding in novel genomes
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
BMC Bioinformatics 2004, 5:59 doi:10.1186/1471-2105-5-59Published: 14 May 2004
Computational gene prediction continues to be an important problem, especially for genomes with little experimental data.
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.
Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.