Introduction

Computational gene prediction continues to be an important problem, especially for genomes with little experimental data.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.Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.

Publications

  1. Gene finding in novel genomes.
    Cite this
    Korf I, 2004-05-01 - BMC bioinformatics

Credits

  1. Ian Korf
    Investigator

    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom of Great Britain and Northern Ireland

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Summary
AccessionBT000527
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Submitted ByIan Korf