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

基本信息

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
项目类别：
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

项目摘要

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、农业和其他生物相关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、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，对它们进行注释是一项困难得多的工作，尤其是对于真核基因组而言。除最简单的真核基因组外，所有真核生物的基因目录仍然不完整，即使对于具有悠久遗传学和分子生物学历史的知名生物体也是如此。由于注释是多种研究和技术应用的焦点，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质量控制基因组注释。该提案描述了我们称为 GenomeInvestigator 的系统的设计。 GenomeInvestigator 由三个组件组成：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 自动针对注释的有问题部分设计实验。与基因组测序类似，MAKER 和 EVALUATOR 生成具有质量值的注释草稿，VERIFIER 指导注释完成工作。 GenomeInvestigator 的设计易于携带，并且可以免费使用。其输出将符合序列本体并兼容 GMOD。医学、农业和其他生物相关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、更便宜、更有营养的食物，以及更少浪费的材料和能源。