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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,...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2004
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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 |
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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 |