Colorado State University, Fort Collins, CO, USA.
The Ohio State University, Columbus, OH, USA.
Bioinformatics. 2023 Apr 3;39(4). doi: 10.1093/bioinformatics/btad110.
Microbial genome annotation is the process of identifying structural and functional elements in DNA sequences and subsequently attaching biological information to those elements. DRAM is a tool developed to annotate bacterial, archaeal, and viral genomes derived from pure cultures or metagenomes. DRAM goes beyond traditional annotation tools by distilling multiple gene annotations to genome level summaries of functional potential. Despite these benefits, a downside of DRAM is the requirement of large computational resources, which limits its accessibility. Further, it did not integrate with downstream metabolic modeling tools that require genome annotation. To alleviate these constraints, DRAM and the viral counterpart, DRAM-v, are now available and integrated with the freely accessible KBase cyberinfrastructure. With kb_DRAM users can generate DRAM annotations and functional summaries from microbial or viral genomes in a point-and-click interface, as well as generate genome-scale metabolic models from DRAM annotations.
For kb_DRAM users, the kb_DRAM apps on KBase can be found in the catalog at https://narrative.kbase.us/#catalog/modules/kb_DRAM. For kb_DRAM users, a tutorial workflow with all documentation is available at https://narrative.kbase.us/narrative/129480. For kb_DRAM developers, software is available at https://github.com/shafferm/kb_DRAM.
微生物基因组注释是识别 DNA 序列中结构和功能元素，并随后将生物信息附加到这些元素上的过程。DRAM 是一种用于注释源自纯培养物或宏基因组的细菌、古细菌和病毒基因组的工具。DRAM 通过将多个基因注释提炼到功能潜力的基因组水平摘要，超越了传统的注释工具。尽管有这些好处，但 DRAM 的一个缺点是需要大量的计算资源，这限制了它的可访问性。此外，它没有与需要基因组注释的下游代谢建模工具集成。为了缓解这些限制，DRAM 和对应的病毒版本 DRAM-v 现在可在免费访问的 KBase 网络基础设施中使用和集成。使用 kb_DRAM，用户可以在点击界面中从微生物或病毒基因组生成 DRAM 注释和功能摘要，以及从 DRAM 注释生成基因组规模的代谢模型。
对于 kb_DRAM 用户，KBase 上的 kb_DRAM 应用程序可在 https://narrative.kbase.us/#catalog/modules/kb_DRAM 目录中找到。对于 kb_DRAM 用户，所有文档的教程工作流程可在 https://narrative.kbase.us/narrative/129480 上找到。对于 kb_DRAM 开发人员，软件可在 https://github.com/shafferm/kb_DRAM 上获得。
