利用基因邻域内的基因功能相似性评估基因组注释。
Assessment of genome annotation using gene function similarity within the gene neighborhood.
作者信息
Jun Se-Ran, Nookaew Intawat, Hauser Loren, Gorin Andrey
机构信息
Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
出版信息
BMC Bioinformatics. 2017 Jul 19;18(1):345. doi: 10.1186/s12859-017-1761-2.
BACKGROUND
Functional annotation of bacterial genomes is an obligatory and crucially important step of information processing from the genome sequences into cellular mechanisms. However, there is a lack of computational methods to evaluate the quality of functional assignments.
RESULTS
We developed a genome-scale model that assigns Bayesian probability to each gene utilizing a known property of functional similarity between neighboring genes in bacteria.
CONCLUSIONS
Our model clearly distinguished true annotation from random annotation with Bayesian annotation probability >0.95. Our model will provide a useful guide to quantitatively evaluate functional annotation methods and to detect gene sets with reliable annotations.
背景
细菌基因组的功能注释是从基因组序列到细胞机制信息处理中必不可少且至关重要的一步。然而，目前缺乏评估功能分配质量的计算方法。
结果
我们开发了一种基因组规模的模型，利用细菌中相邻基因间功能相似性的已知特性，为每个基因赋予贝叶斯概率。
结论
我们的模型通过贝叶斯注释概率>0.95，能够清晰地区分真实注释和随机注释。我们的模型将为定量评估功能注释方法以及检测具有可靠注释的基因集提供有用的指导。
相似文献
BMC Bioinformatics. 2017-7-19
Nucleic Acids Res. 2005-5-18
Methods Mol Biol. 2009
BMC Bioinformatics. 2013-6-1
BMC Bioinformatics. 2004-6-9
BMC Genomics. 2015-12-24
BMC Bioinformatics. 2009-10-8
引用本文的文献
Front Genet. 2022-4-4
PLoS Comput Biol. 2020-11
本文引用的文献
Stand Genomic Sci. 2014-12-8
Nucleic Acids Res. 2013-12-6
Nucleic Acids Res. 2013-11-27
Proc Natl Acad Sci U S A. 2013-11-25
Nucleic Acids Res. 2013-11-18
Nucleic Acids Res. 2013-11-12
Nucleic Acids Res. 2013-11-7
Zotero 插件