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. Conclusion: Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder. Background Complete genomic sequences are becoming more and more abundant. Given a new genome, one of the first and most important tasks is determining the structure of its protein-coding genes. Ab initio gene prediction plays a critical ro...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Ian Korf
• Keywords: BMCBI 2004, Foreign Gene Finders, Gene Finder, Genome