INPHARED_DATABASE

inphared.pl (INfrastructure for a PHAge REference Database) is a perl script which downloads and filters phage genomes from Genbank to provide the most complete phage genome database possible.Useful information, including viral taxonomy and bacterial host data, is extracted from the Genbank files and provided in a summary table. Genes are called on the genomes using Prokka and this output is used to gather metrics which are summarised in the output files, as well as useful input files for vConTACT2. The data provided is all genomes up to Jan 2021. This can be downloaded so users do not have to repeat the process of consistent gene calling on existing genomes. The folder GenomesDB contains subfolders each containing a subfolder that is named on the accession number of each phage. Within each folder are re-called genes in the following format *.ffn*.faa The complete genome *fna and genbank file without any annotation *gbf See https://github.com/RyanCook94/<br><br><br><br><br><br>

inphared.pl（INfrastructure for a PHAge Reference Database，噬菌体参考数据库基础设施）是一款Perl脚本，可从GenBank（美国国立生物技术信息中心核酸序列数据库）中下载并筛选噬菌体基因组，以构建尽可能完整的噬菌体基因组数据库。该脚本可从GenBank文件中提取包括病毒分类学、细菌宿主信息在内的实用信息，并将其整理为汇总表格。该脚本使用Prokka对基因组进行基因调用（编码基因识别），基于该基因预测结果生成多项统计指标，这些指标将与可用于vConTACT2的输入文件一同整合至输出文件中。本次发布的数据集涵盖2021年1月之前收录的全部噬菌体基因组，用户可直接下载该数据集，无需重复对现有基因组开展标准化的基因调用流程。GenomesDB文件夹下包含若干子目录，每个子目录均以对应噬菌体的登录号命名。每个子目录内包含以下格式的文件：重新预测得到的基因文件（*.ffn、*.faa）、完整基因组序列文件（*.fna）以及无任何额外注释的GenBank格式文件（*.gbf）。相关资源可访问 https://github.com/RyanCook94/ 获取。