Software for the creation and quality control of genome annotations

描述(申请人提供)：医药、农业和其他与生物相关的行业越来越依赖于基因组DNA中包含的信息。提高我们对基因结构和调控方式的理解，最终将导致抗击癌症和其他疾病的新疗法，更便宜、更有营养的食物，以及更少浪费的材料和能源。基因组测序现在是一项相对简单的任务。然而，事实证明，对它们进行注释要困难得多，尤其是对真核基因组而言。除了最简单的真核生物基因组外，所有生物的基因目录仍然不完整，即使是具有悠久遗传学和分子生物学历史的知名生物也是如此。由于注释是许多类型研究和技术应用的焦点，因此它们必须是正确的。不完整和不正确的注释毒化了使用它们的每一个实验。我们认为，改进基因组注释的关键在于更好地创建和控制基因组注释的软件。这份提案描述了我们对一个名为GenomeInvestigator的系统的设计。GenomeInvestigator由三个组件组成：制造者、评估者和验证者。Maker创建基因组注释，Evaluator对现有注释执行质量控制分析，Verator自动为注释的有问题部分设计实验。通过类似于基因组测序，制造者和评估者产生具有质量值的草稿注释，而验证者指导注释完成工作。GenomeInvestigator设计为便于携带，并将免费提供。它的输出将是符合序列本体和GMOD的。 医药、农业和其他与生物相关的行业越来越依赖于基因组DNA中包含的信息。提高我们对基因结构和调控方式的理解，最终将导致抗击癌症和其他疾病的新疗法，更便宜、更有营养的食物，以及更少浪费的材料和能源。

DESCRIPTION (provided by applicant): Medicine, agriculture, and other biology-related industries increasingly depend on the information contained in genomic DNA. Advancing our understanding of how genes are structured and regulated will eventually lead to novel therapeutics for combating cancer and other diseases, to cheaper and more nutritious food, and to less wasteful materials and energy sources. Sequencing genomes is now a relatively straightforward task. Annotating them, however, is proving to be a much more difficult one, especially for eukaryotic genomes. The gene catalogs of all but the simplest eukaryotic genomes are still incomplete, even for well-known organisms with a long history of genetics and molecular biology. Because annotations are the focal point for many kinds of research and technological applications, it is essential that they be correct. Incomplete and incorrect annotations poison every experiment that employs them. We believe the key to improving genome annotation lies in better software for the creation and quality control of genome annotations. This proposal describes our design for a system we call GenomeInvestigator. GenomeInvestigator consists of three components: MAKER, EVALUATOR and VERIFIER. MAKER creates genome annotations, EVALUATOR performs quality control analyses on extant annotations, and VERIFIER automatically designs experiments to problematic portions of annotations. By analogy to genome sequencing, MAKER and EVALUATOR produce draft annotation with quality values, and VERIFIER directs annotation finishing efforts. GenomeInvestigator is designed to be easily portable and will be freely available. Its outputs will be Sequence Ontology compliant and GMOD compatible. Medicine, agriculture, and other biology-related industries increasingly depend on the information contained in genomic DNA. Advancing our understanding of how genes are structured and regulated will eventually lead to novel therapeutics for combating cancer and other diseases, to cheaper and more nutritious food, and to less wasteful materials and energy sources.