Cargando…

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,...

Descripción completa

Detalles Bibliográficos
Autor principal: Korf, Ian
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2004
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC421630/
https://www.ncbi.nlm.nih.gov/pubmed/15144565
http://dx.doi.org/10.1186/1471-2105-5-59
_version_ 1782121486109114368
author Korf, Ian
author_facet Korf, Ian
author_sort Korf, Ian
collection PubMed
description 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.
format Text
id pubmed-421630
institution National Center for Biotechnology Information
language English
publishDate 2004
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-4216302004-06-11 Gene finding in novel genomes Korf, Ian BMC Bioinformatics Research Article 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. BioMed Central 2004-05-14 /pmc/articles/PMC421630/ /pubmed/15144565 http://dx.doi.org/10.1186/1471-2105-5-59 Text en Copyright © 2004 Korf; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
spellingShingle Research Article
Korf, Ian
Gene finding in novel genomes
title Gene finding in novel genomes
title_full Gene finding in novel genomes
title_fullStr Gene finding in novel genomes
title_full_unstemmed Gene finding in novel genomes
title_short Gene finding in novel genomes
title_sort gene finding in novel genomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC421630/
https://www.ncbi.nlm.nih.gov/pubmed/15144565
http://dx.doi.org/10.1186/1471-2105-5-59
work_keys_str_mv AT korfian genefindinginnovelgenomes