SAFPredDB: Bacterial synteny database

SAFPredDB is a bacterial synteny database built for the gene function prediction tool SAFPred, Synteny Aware Function Predictor. The database is a collection of conserved synteny and operons found across the bacterial kingdom. First, we formulated a synteny model based on experimentally known operons and the genomic features common in bacteria. We designed a bottoms-up, purely computational approach to build our database based on the proposed synteny model using complete bacterial genome assemblies from the Genome Taxonomy Database (GTDB).<br>Although we initially built SAFPred for our prediction tool only, it can be used for other purposes where such a catalog is needed. As a standalone database, it can be queried to mine information about conserved genomic patterns in bacteria. In addition, it can be updated as newer assemblies are added to GTDB.SAFPredDB是为基因功能预测工具SAFPred（Synteny Aware Function Predictor，共线性感知功能预测器）构建的细菌共线性数据库。该数据库收录了遍布整个细菌界的保守共线性区域与操纵子。 首先，研究团队基于实验验证的操纵子与细菌通用的基因组特征，构建了共线性模型。随后，依托该提出的共线性模型，研究团队采用自下而上的纯计算方法，利用基因组分类数据库（Genome Taxonomy Database, GTDB）中的完整细菌基因组组装数据完成了本数据库的搭建。 尽管本数据库最初仅为配套我们的SAFPred预测工具开发，但它亦可应用于其他需要此类基因组目录的研究场景。作为独立数据库，用户可通过查询该库挖掘细菌保守基因组模式的相关信息。此外，当基因组分类数据库（GTDB）新增基因组组装数据时，本数据库也可同步更新。