Gene finding in novel genomes

BMC Bioinformatics. 2004 May 14;5:59. doi: 10.1186/1471-2105-5-59.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Arabidopsis / genetics
  • Caenorhabditis elegans / genetics
  • Computational Biology / methods
  • Databases, Genetic
  • Drosophila melanogaster / genetics
  • Genes / genetics*
  • Genes, Helminth / genetics
  • Genes, Insect / genetics
  • Genes, Plant / genetics
  • Genetic Variation / genetics
  • Genome*
  • Genome, Plant
  • Predictive Value of Tests
  • Software