MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
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DOI：
10.1101/gr.6743907
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发表时间：
2008-01-01
期刊：
影响因子：
7
通讯作者：
Yandell, Mark
中科院分区：
文献类型：
--
作者：
Cantarel, Brandi L.;Korf, Ian;Yandell, Mark
我们已经开发了一个便携式和易于配置的基因组注释管道称为MAKER。其目的是让研究人员能够独立地注释真核生物基因组并创建基因组数据库。MAKER识别重复序列，将EST和蛋白质与基因组对齐，产生从头基因预测，并自动将这些数据合成为具有循证质量指数的基因注释。MAKER也很容易训练：初步运行的输出用于自动重新训练其基因预测算法，在后续运行中产生更高质量的基因模型。MAKER的输入是最小的，其输出可用于创建GMOD数据库。它的输出也可以在Apollo Genome浏览器中查看; MAKER的这个功能提供了一种简单的方法来注释，查看和编辑单个重叠群和BAC，而无需数据库的开销。作为原理的证明，我们已经使用MAKER注释了涡虫Schmidtea mediterranea的基因组，并创建了一个新的基因组数据库SmedGD。我们还将MAKER的性能与其他已发布的注释管道进行了比较。我们的研究结果表明，MAKER提供了一个简单而有效的手段，将基因组序列转化为社区可访问的基因组数据库。MAKER应该被证明对新兴的模式生物基因组项目特别有用，因为这些项目可能不容易获得广泛的生物信息学资源。
We have developed a portable and easily configurable genome annotation pipeline called MAKER. Its purpose is to allow investigators to independently annotate eukaryotic genomes and create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions, and automatically synthesizes these data into gene annotations having evidence-based quality indices. MAKER is also easily trainable: Outputs Of preliminary runs are used to automatically retrain its gene-prediction algorithm, producing higher-quality gene-models on subsequent runs. MAKER's inputs are minimal, and its outputs can be used to create a GMOD database. Its Outputs can also be viewed in the Apollo Genome browser; this feature of MAKER provides an easy means to annotate, view, and edit individual contigs and BACs without the overhead of a database. As proof of principle, we have used MAKER to annotate the genome of the planarian Schmidtea mediterranea and to create a new genome database, SmedGD. We have also compared MAKER's performance to other published annotation pipelines. Our results demonstrate that MAKER provides a simple and effective means to convert a genome sequence into a community-accessible genome database. MAKER should prove especially useful for emerging model Organism genome projects for which extensive bioinformatics resources may not be readily available.