ABI: Development Implementing Galaxy for Community-based Phage Genomics

噬菌体是细菌的病毒，是生物圈中数量最多的遗传实体，数量是细菌的10-100倍，并且包含了大部分的DNA多样性。噬菌体生物学是全球生态学和基因转移全球动态的驱动力。噬菌体作为细菌的天然捕食者，在人类健康和畜牧业和农业中具有公认的抗菌剂潜力。噬菌体，因为它们可以被限制在特定的细菌物种或属，代表了目前唯一可用的工具，用于操纵微生物组中的不同细菌种群，现在已知微生物组是健康和发展的重要组成部分。尽管有所有这些因素，但只有一小部分噬菌体生物多样性被测序的基因组捕获;事实上，噬菌体是迄今为止测序最少的遗传实体。随着下一代测序技术的发展，噬菌体DNA序列的流动将大大增加。然而，噬菌体基因组代表了基因组分析中的特殊问题，部分原因是生物学因素，包括快速序列分歧，基因大小的压缩和广泛的基因重叠。更大的问题是普遍缺乏噬菌体生物学方面的专业知识，这使得大多数科学公众无法获得噬菌体基因组的高质量注释。该项目将为生物信息学分析建立可扩展的基础设施，重点是噬菌体的自动结构和功能注释。将开发和部署公共可访问的基础设施，从新的和现有的组件，以支持社区重新注释的范式转换为“黄金标准”策划的注释集。此外，随着噬菌体基因组学领域的迅速扩大，该基础设施将开发专注于未来新噬菌体基因组的获取和注释的组件。将开发和发布编码专家注释知识的工具，以提高自动化、质量、噬菌体注释的最新水平。整个项目将在OSI批准的许可证下作为开源软件开发，允许在其他基因组注释社区重新实施该项目的基础设施，并提供价值。噬菌体基因组学教育资源开发作为我们在噬菌体基因组学在TAMU完善的课程的一部分将得到改善，以利用正在建设的新的社区资源。随着实施的进展，部署的基础架构和进度更新将在https://cpt.tamu.edu/phagedb/上提供

Phages, the viruses of bacteria, are the most numerous genetic entities in the biosphere, outnumbering bacteria by 10-100-fold, and contain most of its DNA diversity. Phage biology is a driver in global ecology and in the global dynamics of gene transfer. Phages, as the natural predators of bacteria, have recognized potential as antibacterial agents, both in human health and in animal husbandry and agriculture. Phages, because they can be restricted to specific bacterial species or genera, represent the only currently available tool for manipulating the diverse populations of bacteria in microbiomes, now known to be an essential component of health and development. Despite all of these factors, only a tiny fraction of phage biodiversity is captured by sequenced genomes; in fact, phages are by far the most under-sequenced genetic entity. As Next Generation Sequencing advances, the flow of phage DNA sequence is going to increase enormously. However, phage genomes represent special problems in genomic analysis, in part because of biological factors, including rapid sequence divergence, the compression of gene sizes and extensive gene overlap. Even more problematic is the general lack of expertise in phage biology, which makes quality annotation of phage genomes inaccessible to most of the scientific public.The project will implement scalable infrastructure for bioinformatics analyses, focusing on the automated structural and functional annotation of phages. Publicly accessible infrastructure will be developed and deployed, from new and existing components to support community re-annotation of paradigm phages into "gold standard" curated annotation sets. Additionally the infrastructure will develop components focused on the acquisition and annotation of new phage genomes going forward, as the field of bacteriophage genomics rapidly expands. Tools will be developed and released encoding expert annotation knowledge to improve the state of the art in automated, quality, phage annotation. The entire project will be developed as open source software under an OSI approved license, permitting the re-implementation of the project's infrastructure in other genome annotation communities where it will provide value. Phage Genomics Education resources developed as part of our well-established course in Phage Genomics at TAMU will be improved to take advantage of the new community resources being built. As implementation progresses, the infrastructure deployed and progress updates will be available at https://cpt.tamu.edu/phagedb/