Gene finding in novel genomes

Research output: Contribution to journalArticle

892 Scopus citations

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 dedicated gene finder.

Original languageEnglish (US)
Article number59
JournalBMC Bioinformatics
Volume5
DOIs
StatePublished - May 14 2004
Externally publishedYes

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

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