State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.
College of Computer and Information Science, Chongqing Normal University, Chongqing, China.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz025.
Pasteurella multocida can infect a wide range of host, including humans and animals of economic importance. Genomics studies on the pathogen have produced a large amount of omics data, which are deposited in GenBank but lacks a dedicated and comprehensive resource for further analysis and integration so that need to be brought together centrally in a coherent and systematic manner. Here we have collected the genomic data for 176 P. multocida strains that are categorized into 11 host groups and 9 serotype groups, and developed the open-access P. multocida Database (PamulDB) to make this resource readily available. The PamulDB implements and integrates Chado for genome data management, Drupal for web content management, and bioinformatics tools like NCBI BLAST, HMMER, PSORTb and OrthoMCL for data analysis. All the P. multocida genomes have been further annotated for search and analysis of homologous sequence, phylogeny, gene ontology, transposon, protein subcellular localization and secreted protein. Transcriptomic data of P. multocida are also selectively adopted for gene expression analysis. The PamulDB has been developing and improving to better aid researchers with identifying and classifying of pathogens, dissecting mechanisms of the pathogen infection and host response.
多杀巴斯德菌可以感染范围广泛的宿主，包括人类和具有重要经济价值的动物。对该病原体的基因组学研究产生了大量的组学数据，这些数据被存入 GenBank，但缺乏专门的、全面的资源来进行进一步的分析和整合，因此需要以连贯和系统的方式集中在一起。在这里，我们收集了 176 株多杀巴斯德菌的基因组数据，这些菌株分为 11 个宿主群和 9 个血清型群，并开发了开放获取的多杀巴斯德菌数据库（PamulDB），以便更方便地使用这一资源。PamulDB 实现并整合了 Chado 进行基因组数据管理、Drupal 进行网络内容管理，以及 NCBI BLAST、HMMER、PSORTb 和 OrthoMCL 等生物信息学工具用于数据分析。所有多杀巴斯德菌基因组都经过进一步注释，以便于搜索和分析同源序列、系统发育、基因本体、转座子、蛋白质亚细胞定位和分泌蛋白。多杀巴斯德菌的转录组数据也被选择性地用于基因表达分析。PamulDB 一直在不断发展和改进，以更好地帮助研究人员识别和分类病原体，剖析病原体感染和宿主反应的机制。
