Enzyme-specific profiles for genome annotation: PRIAM
Enzyme-specific profiles for genome annotation: PRIAM
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DOI：
10.1093/nar/gkg847
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发表时间：
2003-11-15
影响因子：
14.9
通讯作者：
Kahn, D
中科院分区：
文献类型：
--
作者：
Claudel-Renard, C;Chevalet, C;Kahn, D
完全测序的基因组的出现为在鉴定酶编码基因的基础上重建代谢途径开辟了道路。在这里，我们描述了PRIAM，一种在完全测序的基因组中自动化酶检测的方法，基于酶数据库中的酶分类。PRIAM依赖于为每个酶条目自动定制的位置特异性评分矩阵（“配置文件”）集。自动生成的逻辑规则定义需要这些配置文件中的哪一个，以推断生物体中相应酶的存在。作为一个例子，PRIAM被应用于从固氮细菌苜蓿中华根瘤菌的全基因组中鉴定潜在的代谢途径。将这种自动化方法的结果与原始基因组注释进行比较，并在KEGG图上可视化，以便于解释代谢途径并突出潜在缺失的酶。
The advent of fully sequenced genomes opens the ground for the reconstruction of metabolic pathways on the basis of the identification of enzyme-coding genes. Here we describe PRIAM, a method for automated enzyme detection in a fully sequenced genome, based on the classification of enzymes in the ENZYME database. PRIAM relies on sets of position-specific scoring matrices ('profiles') automatically tailored for each ENZYME entry. Automatically generated logical rules define which of these profiles is required in order to infer the presence of the corresponding enzyme in an organism. As an example, PRIAM was applied to identify potential metabolic pathways from the complete genome of the nitrogen-fixing bacterium Sinorhizobium meliloti. The results of this automated method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of metabolic pathways and to highlight potentially missing enzymes.