Zhou C E, Smith J, Lam M, Zemla A, Dyer M D, Slezak T
Pathogen Bioinformatics, Mailstop L-174 Energy, Environment, and Biology Division, Computations Directorate, Lawrence Livermore National Laboratory, 70000 East Avenue, Livermore, CA 94550, USA.
Nucleic Acids Res. 2007 Jan;35(Database issue):D391-4. doi: 10.1093/nar/gkl791. Epub 2006 Nov 7.
Knowledge of toxins, virulence factors and antibiotic resistance genes is essential for bio-defense applications aimed at identifying 'functional' signatures for characterizing emerging or engineered pathogens. Whereas genetic signatures identify a pathogen, functional signatures identify what a pathogen is capable of. To facilitate rapid identification of sequences and characterization of genes for signature discovery, we have collected all publicly available (as of this writing), organized sequences representing known toxins, virulence factors, and antibiotic resistance genes in one convenient database, which we believe will be of use to the bio-defense research community. MvirDB integrates DNA and protein sequence information from Tox-Prot, SCORPION, the PRINTS virulence factors, VFDB, TVFac, Islander, ARGO and a subset of VIDA. Entries in MvirDB are hyperlinked back to their original sources. A blast tool allows the user to blast against all DNA or protein sequences in MvirDB, and a browser tool allows the user to search the database to retrieve virulence factor descriptions, sequences, and classifications, and to download sequences of interest. MvirDB has an automated weekly update mechanism. Each protein sequence in MvirDB is annotated using our fully automated protein annotation system and is linked to that system's browser tool. MvirDB can be accessed at http://mvirdb.llnl.gov/.
对于旨在识别用于表征新出现或工程化病原体的“功能”特征的生物防御应用而言，了解毒素、毒力因子和抗生素抗性基因至关重要。遗传特征可识别病原体，而功能特征则能确定病原体的能力。为便于快速识别序列并对用于特征发现的基因进行表征，我们收集了所有公开可用的（截至撰写本文时）、代表已知毒素、毒力因子和抗生素抗性基因的有组织序列，并将其整合到一个便捷的数据库中，我们相信该数据库将对生物防御研究界有所帮助。MvirDB整合了来自Tox-Prot、SCORPION、PRINTS毒力因子、VFDB、TVFac、Islander、ARGO以及VIDA子集的DNA和蛋白质序列信息。MvirDB中的条目超链接回其原始来源。一个blast工具允许用户对MvirDB中的所有DNA或蛋白质序列进行blast搜索，一个浏览器工具允许用户搜索数据库以检索毒力因子描述、序列和分类，并下载感兴趣的序列。MvirDB具有每周自动更新机制。MvirDB中的每个蛋白质序列都使用我们的全自动蛋白质注释系统进行注释，并链接到该系统的浏览器工具。可通过http://mvirdb.llnl.gov/访问MvirDB。
