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Gene finding in novel genomes

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Korf, Ian·2004·BMC Bioinformatics

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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.

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Authors: Korf, I.
Venue: BMC Bioinformatics
Publisher: Springer Science and Business Media LLC
Published: 2004-05-14
Volume: 5
Issue: 1
Pages: 59-59
ISSN: 1471-2105 (ISSN-L)
DOI: 10.1186/1471-2105-5-59
OpenAlex: W1484347389
Cited by: 3,192
References: 1
FWCI: 6.89
Type: journal article
Language: en
Open access: gold

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Gene finding in novel genomes

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