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Genome Annotation in Plants and Fungi: EuGene as a Model Platform

机译:植物和真菌中的基因组注释:以EuGene为模型平台

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In this era of whole genome sequencing, reliable genome annotations (identification of functional regions) are the cornerstones for many subsequent analyses. Not only is careful annotation important for studying the gene and gene family content of a genome and its host, but also for wide-scale transcriptome and proteome analyses attempting to describe a certain biological process or to get a global picture of a cell's behavior. Although the number of sequenced genomes is increasing thanks to the application of new technologies, genome-wide analyses will critically depend on the quality of the genome annotations. However, the annotation process is more complicated in the plant field than in the animal field because of the limited funding that leads to much fewer experimental data and less annotation expertise. This situation calls for highly automated annotation platforms that can make the best use of all available data, experimental or not. We discuss how the gene prediction (the process of predicting protein gene structures in genomic sequences) research field increasingly shifts from methods that typically exploited one or two types of data to more integrative approaches that simultaneously deal with various experimental, statistical, or other in silico evidence. We illustrate the importance of integrative approaches for producing high-quality automatic annotations of genomes of plants and algae as well as of fungi that live in close association with plants using the platform EuGène as an example.
机译:在整个基因组测序的时代,可靠的基因组注释(功能区的识别)是许多后续分析的基石。仔细的注释不仅对于研究基因组及其宿主的基因和基因家族内容非常重要,而且对于试图描述某种生物学过程或获得细胞行为的全局图片的大规模转录组和蛋白质组分析也很重要。尽管由于新技术的应用,测序基因组的数量正在增加,但是全基因组范围的分析将严格取决于基因组注释的质量。但是,由于经费有限,注释过程在植物领域比在动物领域更为复杂,这导致更少的实验数据和更少的注释专业知识。这种情况需要高度自动化的注释平台,该平台可以充分利用所有可用数据(无论是否经过实验)。我们讨论了基因预测(预测基因组序列中蛋白质基因结构的过程)研究领域如何从通常利用一种或两种类型数据的方法转变为同时处理各种实验,统计或其他计算机模拟的更综合的方法证据。我们以平台EuGène为例,说明了整合方法对于产生高质量的植物和藻类以及与植物紧密相关的真菌基因组的自动注释的重要性。

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