Gene finding in novel genomes.

by: I Korf

BMC Bioinformatics, Vol. 5 (14 May 2004)

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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 a dedicated gene finder.

@article{citeulike:311557, 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 a dedicated gene finder.}, address = {Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. ik1@sanger.ac.uk}, author = {Korf, I. }, citeulike-article-id = {311557}, doi = {http://dx.doi.org/10.1186/1471-2105-5-59}, issn = {1471-2105}, journal = {BMC Bioinformatics}, keywords = {gene, prediction}, month = {May}, posted-at = {2007-07-15 13:51:00}, priority = {2}, title = {Gene finding in novel genomes.}, url = {http://dx.doi.org/10.1186/1471-2105-5-59}, volume = {5}, year = {2004} }

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TY - JOUR ID - citeulike:311557 L3 - citeulike-article-id:311557 TI - Gene finding in novel genomes. JF - BMC Bioinformatics VL - 5 AD - Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. ik1@sanger.ac.uk SN - 1471-2105 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 a dedicated gene finder. KW - gene KW - prediction AU - Korf, I PY - 2004/05/14/ UR - http://dx.doi.org/10.1186/1471-2105-5-59 ER -

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