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Consistency of gene starts among Burkholderia genomes
BACKGROUND: Evolutionary divergence in the position of the translational start site among orthologous genes can have significant functional impacts. Divergence can alter the translation rate, degradation rate, subcellular location, and function of the encoded proteins. RESULTS: Existing Genbank gene...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2011
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3049151/ https://www.ncbi.nlm.nih.gov/pubmed/21342528 http://dx.doi.org/10.1186/1471-2164-12-125 |
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author | Dunbar, John Cohn, Judith D Wall, Michael E |
author_facet | Dunbar, John Cohn, Judith D Wall, Michael E |
author_sort | Dunbar, John |
collection | PubMed |
description | BACKGROUND: Evolutionary divergence in the position of the translational start site among orthologous genes can have significant functional impacts. Divergence can alter the translation rate, degradation rate, subcellular location, and function of the encoded proteins. RESULTS: Existing Genbank gene maps for Burkholderia genomes suggest that extensive divergence has occurred--53% of ortholog sets based on Genbank gene maps had inconsistent gene start sites. However, most of these inconsistencies appear to be gene-calling errors. Evolutionary divergence was the most plausible explanation for only 17% of the ortholog sets. Correcting probable errors in the Genbank gene maps decreased the percentage of ortholog sets with inconsistent starts by 68%, increased the percentage of ortholog sets with extractable upstream intergenic regions by 32%, increased the sequence similarity of intergenic regions and predicted proteins, and increased the number of proteins with identifiable signal peptides. CONCLUSIONS: Our findings highlight an emerging problem in comparative genomics: single-digit percent errors in gene predictions can lead to double-digit percentages of inconsistent ortholog sets. The work demonstrates a simple approach to evaluate and improve the quality of gene maps. |
format | Text |
id | pubmed-3049151 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-30491512011-03-06 Consistency of gene starts among Burkholderia genomes Dunbar, John Cohn, Judith D Wall, Michael E BMC Genomics Research Article BACKGROUND: Evolutionary divergence in the position of the translational start site among orthologous genes can have significant functional impacts. Divergence can alter the translation rate, degradation rate, subcellular location, and function of the encoded proteins. RESULTS: Existing Genbank gene maps for Burkholderia genomes suggest that extensive divergence has occurred--53% of ortholog sets based on Genbank gene maps had inconsistent gene start sites. However, most of these inconsistencies appear to be gene-calling errors. Evolutionary divergence was the most plausible explanation for only 17% of the ortholog sets. Correcting probable errors in the Genbank gene maps decreased the percentage of ortholog sets with inconsistent starts by 68%, increased the percentage of ortholog sets with extractable upstream intergenic regions by 32%, increased the sequence similarity of intergenic regions and predicted proteins, and increased the number of proteins with identifiable signal peptides. CONCLUSIONS: Our findings highlight an emerging problem in comparative genomics: single-digit percent errors in gene predictions can lead to double-digit percentages of inconsistent ortholog sets. The work demonstrates a simple approach to evaluate and improve the quality of gene maps. BioMed Central 2011-02-22 /pmc/articles/PMC3049151/ /pubmed/21342528 http://dx.doi.org/10.1186/1471-2164-12-125 Text en Copyright ©2011 Dunbar et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Dunbar, John Cohn, Judith D Wall, Michael E Consistency of gene starts among Burkholderia genomes |
title | Consistency of gene starts among Burkholderia genomes |
title_full | Consistency of gene starts among Burkholderia genomes |
title_fullStr | Consistency of gene starts among Burkholderia genomes |
title_full_unstemmed | Consistency of gene starts among Burkholderia genomes |
title_short | Consistency of gene starts among Burkholderia genomes |
title_sort | consistency of gene starts among burkholderia genomes |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3049151/ https://www.ncbi.nlm.nih.gov/pubmed/21342528 http://dx.doi.org/10.1186/1471-2164-12-125 |
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