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：
7814003
负责人：
Mark Douglas Yandell
金额：
$ 55.57万
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/7814003
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，农业和其他与生物学相关的行业越来越取决于基因组DNA中包含的信息。促进我们对基因结构和调节方式的理解最终将导致新颖的治疗疗法，以打击癌症和其他疾病，更便宜，更营养的食物，以及浪费的材料和能源较少。现在，测序基因组是一个相对简单的任务。但是，对它们的注释被证明是一个更加困难的，尤其是对于真核基因组。除了最简单的真核基因组以外的所有基因目录仍然不完整，即使对于著名的遗传学和分子生物学史的著名生物体也是如此。由于注释是多种研究和技术应用的焦点，因此它们是正确的。不完整和不正确的注释毒害了每个实验的每个实验。我们认为，改善基因组注释的关键在于更好的软件来创建基因组注释的质量控制。该提案描述了我们称为基因组评估器的系统的设计。 GenomeInvestigator由三个组成部分组成：制造商，评估器和验证者。制造商创建基因组注释，评估者对现有注释进行质量控制分析，而验证者会自动将实验设计为有问题的注释部分。通过类似于基因组测序，制造商和评估者用质量值生成草稿，而验证者则指导注释完成工作。 Genome Investigator设计为容易便携式，并且将是免费的。它的输出将符合序列本体论和GMOD兼容。医学，农业和其他与生物学相关的行业越来越多地取决于基因组DNA中包含的信息。促进我们对基因结构和调节方式的理解最终将导致新颖的治疗疗法，以打击癌症和其他疾病，更便宜，更营养的食物，以及浪费的材料和能源较少。