Gene finding in novel genomes.
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.


CONCLUSIONS
Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.
Korf
Ian
I
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. ik1@sanger.ac.uk
D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D017173:Caenorhabditis elegans / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics; D005796:Genes / Q000235:genetics*; D017238:Genes, Helminth / Q000235:genetics; D017344:Genes, Insect / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D016678:Genome; D018745:Genome, Plant; D011237:Predictive Value of Tests; D012984:Software