MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.
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DOI：
10.1186/1471-2105-12-491
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发表时间：
2011-12-22
影响因子：
3
通讯作者：
Yandell M
中科院分区：
文献类型：
--
作者：
Holt C;Yandell M
第二代测序技术正在引发关于正在测序的基因组类型以及如何注释它们的重大转变。虽然第一代基因组计划的重点是经过充分研究的模式生物，但今天的许多项目涉及基因组在很大程度上是未知领域的外来生物。这使得他们的注释变得复杂，因为与第一代项目不同，没有预先存在的“黄金标准”基因模型来训练基因发现者。基因组组装的改进和mRNA-seq数据的广泛可用性也为更新和重新注释先前发表的基因组注释创造了机会。因此，今天的基因组计划需要新的基因组注释工具，以应对第二代测序技术带来的挑战和机遇。我们提出了MAKER 2，一个基因组注释和数据管理工具，专为第二代基因组计划。MAKER 2是一个多线程的并行应用程序，可以处理几乎任何大小的第二代数据集。我们表明，MAKER 2可以为训练数据有限、质量低甚至不存在的新基因组产生准确的注释。MAKER 2还提供了一种使用mRNA-seq数据来提高注释质量的简单方法;它可以使用这些数据来更新传统注释，显着提高其质量。我们还表明，MAKER 2可以评估基因组注释的质量，并识别和优先考虑人工审查的问题注释。MAKER 2是第一个专门为第二代基因组计划设计的注释引擎。MAKER 2可以扩展到任何大小的数据集，几乎不需要训练数据，并且可以使用mRNA-seq数据来提高注释质量。它还可以更新和管理遗留基因组注释数据集。
Second-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated. While the first generation of genome projects focused on well-studied model organisms, many of today's projects involve exotic organisms whose genomes are largely terra incognita. This complicates their annotation, because unlike first-generation projects, there are no pre-existing 'gold-standard' gene-models with which to train gene-finders. Improvements in genome assembly and the wide availability of mRNA-seq data are also creating opportunities to update and re-annotate previously published genome annotations. Today's genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies. We present MAKER2, a genome annotation and data management tool designed for second-generation genome projects. MAKER2 is a multi-threaded, parallelized application that can process second-generation datasets of virtually any size. We show that MAKER2 can produce accurate annotations for novel genomes where training-data are limited, of low quality or even non-existent. MAKER2 also provides an easy means to use mRNA-seq data to improve annotation quality; and it can use these data to update legacy annotations, significantly improving their quality. We also show that MAKER2 can evaluate the quality of genome annotations, and identify and prioritize problematic annotations for manual review. MAKER2 is the first annotation engine specifically designed for second-generation genome projects. MAKER2 scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality. It can also update and manage legacy genome annotation datasets.
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影响因子：
14.9
作者：
Benson DA;Karsch-Mizrachi I;Lipman DJ;Ostell J;Sayers EW
通讯作者：
Sayers EW
影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
4.5
作者：
Baxter SW;Nadeau NJ;Maroja LS;Wilkinson P;Counterman BA;Dawson A;Beltran M;Perez-Espona S;Chamberlain N;Ferguson L;Clark R;Davidson C;Glithero R;Mallet J;McMillan WO;Kronforst M;Joron M;Ffrench-Constant RH;Jiggins CD
通讯作者：
Jiggins CD
Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
DOI：
10.1073/pnas.0337561100
发表时间：
2003-02-04
影响因子：
11.1
作者：
Guigó, R;Dermitzakis, ET;Brent, MR
通讯作者：
Brent, MR