Department of Biology, James Madison University, 820 Madison Dr, MSC 7801, Harrisonburg, VA 22807 USA.
BMC Bioinformatics. 2011 Oct 12;12:395. doi: 10.1186/1471-2105-12-395.
Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation.
We describe here a bioinformatic tool, Phamerator, that assorts protein-coding genes into phamilies of related sequences using pairwise comparisons to generate a database of gene relationships. This database is used to generate genome maps of multiple phages that incorporate nucleotide and amino acid sequence relationships, as well as genes containing conserved domains. Phamerator also generates phamily circle representations of gene phamilies, facilitating analysis of the different evolutionary histories of individual genes that migrate through phage populations by horizontal genetic exchange.
Phamerator represents a useful tool for comparative genomic analysis and comparative representations of bacteriophage genomes.
噬菌体基因组具有镶嵌结构，充满了功能未知的小开放阅读框，这给它们的注释、比较分析和表示带来了挑战。
我们在这里描述了一种生物信息学工具 Phamerator，它使用两两比较将蛋白质编码基因分类为相关序列的 phamilies，从而生成基因关系数据库。该数据库用于生成多个噬菌体的基因组图谱，其中包括核苷酸和氨基酸序列关系以及包含保守结构域的基因。Phamerator 还生成基因 phamilies 的 phamily 循环表示形式，便于通过水平基因交换分析在噬菌体群体中迁移的单个基因的不同进化历史。
Phamerator 是一种用于比较基因组分析和噬菌体基因组比较表示的有用工具。
