Software for the creation and quality control of genome annotations

用于创建和质量控制基因组注释的软件

• 批准号: 7636754
• 负责人: Mark Douglas Yandell
• 金额: $ 54.74万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-06-12 至 2012-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7636754
• 关键词: Address; Agriculture; Amino Acid Sequence; Animal Model; Bioinformatics; Biology; Boxing; Caenorhabditis elegans; Cataloging; Catalogs; Collaborations; Communities; Complex; Computer software; DNA; Data; Databases; Disease; Effectiveness; Energy-Generating Resources; Ensure; Eukaryota; Exons; Expressed Sequence Tags; Food; Genbank; Gene Structure; Genes; Genetic; Genome; Genomics; Individual; Industry; Insect Vectors; Introns; Lead; Malignant Neoplasms; Measures; Medicine; Molecular Biology; Ontology; Organism; Output; Outsourcing; Peptide Sequence Determination; Performance; Poison; Procedures; Protein Isoforms; Proteins; Quality Control; RNA Splicing; Reading; Recording of previous events; Reporting; Research; Research Personnel; Reverse Transcriptase Polymerase Chain Reaction; Risk; Running; Sampling; Scientist; Solutions; Source; System; Technology; Testing; Text; Training; Transcript; Untranslated Regions; base; combat; density; design; falls; genome sequencing; human disease; improved; meetings; model organisms databases; novel; novel therapeutics; research study; software systems; tool; vertebrate genome

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.

描述（由申请人提供）：医学、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。加深我们对基因结构和调控方式的理解，最终将带来对抗癌症和其他疾病的新疗法，带来更便宜、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，尤其是对真核生物基因组而言。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，即使是那些有着悠久遗传学和分子生物学历史的知名生物。由于注释是许多研究和技术应用程序的焦点，因此注释的正确性至关重要。不完整和不正确的注释会毒害每一个使用它们的实验。我们相信改进基因组注释的关键在于更好的软件来创建和控制基因组注释的质量。这个提案描述了我们对一个系统的设计，我们称之为基因组调查员。GenomeInvestigator由三个部分组成：MAKER， EVALUATOR和VERIFIER。MAKER创建基因组注释，EVALUATOR对现有注释进行质量控制分析，VERIFIER自动设计注释中有问题的部分的实验。类似于基因组测序，MAKER和EVALUATOR生成带有质量值的草稿注释，VERIFIER指导注释的完成工作。GenomeInvestigator的设计便于携带，并且可以免费获得。它的输出将是序列本体兼容和GMOD兼容。