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 dedicated gene finder.
| Original language | English (US) |
|---|---|
| Article number | 59 |
| Journal | BMC Bioinformatics |
| Volume | 5 |
| DOIs | |
| State | Published - May 14 2004 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Medicine(all)
- Structural Biology
- Applied Mathematics
Cite this
Gene finding in novel genomes. / Korf, Ian F.
In: BMC Bioinformatics, Vol. 5, 59, 14.05.2004.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Gene finding in novel genomes
AU - Korf, Ian F
PY - 2004/5/14
Y1 - 2004/5/14
N2 - 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 dedicated gene finder.
AB - 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 dedicated gene finder.
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UR - http://www.scopus.com/inward/citedby.url?scp=2942544417&partnerID=8YFLogxK
U2 - 10.1186/1471-2105-5-59
DO - 10.1186/1471-2105-5-59
M3 - Article
C2 - 15144565
AN - SCOPUS:2942544417
VL - 5
JO - BMC Bioinformatics
JF - BMC Bioinformatics
SN - 1471-2105
M1 - 59
ER -