MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
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DOI：
10.1093/nar/gkl723
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发表时间：
2006-11-01
影响因子：
14.9
通讯作者：
Takagi, Toshihisa
中科院分区：
文献类型：
--
作者：
Noguchi, Hideki;Park, Jungho;Takagi, Toshihisa
详尽的基因识别是所有宏基因组学项目中的基本目标。但是，大多数宏基因组序列是未组装的匿名片段，并且不能应用常规的基因调查方法。我们已经开发了一个实质性基因调查程序Metagene，该程序利用了由给定序列的GC含量和其他各种措施估算的Di-Codon频率。 Metagene可以根据几百个碱基的匿名基因组序列预测一系列原核基因，对于人造shot弹枪序列（来自12种的700 bp片段），灵敏度为95％，特异性为90％。 Metagene具有两组密码子频率插值，一组用于细菌，一组用于古细菌，并使用我们建议的域分类方法自动为给定序列选择了适当的集合。域分类正常工作，正确地将域信息分配给了超过90％的人造shot弹枪序列。 Metagene应用于Sargasso Sea数据集，预测了几乎所有注释的基因和显着的新基因。 Metagene可以应用于各种宏基因组项目，并扩大宏基因组学的效用。
Exhaustive gene identification is a fundamental goal in all metagenomics projects. However, most metagenomic sequences are unassembled anonymous fragments, and conventional gene-finding methods cannot be applied. We have developed a prokaryotic gene-finding program, MetaGene, which utilizes di-codon frequencies estimated by the GC content of a given sequence with other various measures. MetaGene can predict a whole range of prokaryotic genes based on the anonymous genomic sequences of a few hundred bases, with a sensitivity of 95% and a specificity of 90% for artificial shotgun sequences (700 bp fragments from 12 species). MetaGene has two sets of codon frequency interpolations, one for bacteria and one for archaea, and automatically selects the proper set for a given sequence using the domain classification method we propose. The domain classification works properly, correctly assigning domain information to more than 90% of the artificial shotgun sequences. Applied to the Sargasso Sea dataset, MetaGene predicted almost all of the annotated genes and a notable number of novel genes. MetaGene can be applied to wide variety of metagenomic projects and expands the utility of metagenomics.