A manual curation strategy to improve genome annotation: application to a set of haloarchael genomes.
A manual curation strategy to improve genome annotation: application to a set of haloarchael genomes.
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DOI：
10.3390/life5021427
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发表时间：
2015-06-02
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通讯作者：
Oesterhelt D
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文献类型：
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作者：
Pfeiffer F;Oesterhelt D
基因组注释错误是一个长期困扰生物科学研究的问题。一个人工管理的努力描述，试图产生高质量的基因组注释的一组盐古菌基因组（盐盐杆菌和Hbt）。湖北火山，火山和Hfx。地中海，法老钠单胞菌和Nmn。moolapensis， Haloquadratum walsbyi菌株HBSQ001和C23， Natrialba magadii， Haloarcula marismortui和Har。海苔属（Halohasta litchfieldiae）。基因组检查缺失的基因，启动密码子错配，和破坏的基因。特定功能的分配最好基于实验表征的同源物（金标准蛋白）。为了避免过度注释（这是数据库错误的主要来源），当对特定基板分配的支持不足时，我们将注释限制为仅对一般函数分配。这种策略的结果是，注释能够抵抗危及公共数据库的大量错误。对来自所调查基因组的同源对的注释一致性进行了严格验证。注释会定期与UniProt数据库进行交叉检查，以进一步改进注释并提高标准化水平。增强的基因组注释被提交到公共数据库（EMBL/GenBank, UniProt），以造福科学界。增强的注释也可以通过HaloLex公开获得。
Genome annotation errors are a persistent problem that impede research in the biosciences. A manual curation effort is described that attempts to produce high-quality genome annotations for a set of haloarchaeal genomes (Halobacterium salinarum and Hbt. hubeiense, Haloferax volcanii and Hfx. mediterranei, Natronomonas pharaonis and Nmn. moolapensis, Haloquadratum walsbyi strains HBSQ001 and C23, Natrialba magadii, Haloarcula marismortui and Har. hispanica, and Halohasta litchfieldiae). Genomes are checked for missing genes, start codon misassignments, and disrupted genes. Assignments of a specific function are preferably based on experimentally characterized homologs (Gold Standard Proteins). To avoid overannotation, which is a major source of database errors, we restrict annotation to only general function assignments when support for a specific substrate assignment is insufficient. This strategy results in annotations that are resistant to the plethora of errors that compromise public databases. Annotation consistency is rigorously validated for ortholog pairs from the genomes surveyed. The annotation is regularly crosschecked against the UniProt database to further improve annotations and increase the level of standardization. Enhanced genome annotations are submitted to public databases (EMBL/GenBank, UniProt), to the benefit of the scientific community. The enhanced annotations are also publically available via HaloLex.