Gene finding in novel genomes.
Ontology highlight
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.
SUBMITTER: Korf I
PROVIDER: S-EPMC421630 | biostudies-literature | 2004 May
REPOSITORIES: biostudies-literature
Publications
<h4>Background</h4>Computational gene prediction continues to be an important problem, especially for genomes with little experimental data.<h4>Results</h4>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 f ...[more]
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