Phamerator: a bioinformatic tool for comparative bacteriophage genomics
Phamerator: a bioinformatic tool for comparative bacteriophage genomics
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DOI：
10.1186/1471-2105-12-395
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发表时间：
2011-10-12
影响因子：
3
通讯作者：
Hatfull, Graham F.
中科院分区：
文献类型：
--
作者：
Cresawn, Steven G.;Bogel, Matt;Hatfull, Graham F.
背景资料：噬菌体基因组具有马赛克结构，充满了小的开放阅读框架的未知功能，在他们的注释，比较分析，和representation.Results提出了挑战：我们在这里描述了一个生物信息学工具，Phamerator，phamilies的相关序列使用成对比较，产生一个数据库的基因关系的phamilies的蛋白质编码基因。该数据库用于生成包含核苷酸和氨基酸序列关系以及包含保守结构域的基因的多个外显子的基因组图谱。Phamerator还产生phamily圈表示的基因phamilies，促进分析不同的进化历史的个别基因，通过噬菌体种群水平的遗传exchanges.Conclusions迁移：Phamerator是一个有用的工具，用于比较基因组分析和比较表示的噬菌体基因组。
Background: 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.Results: 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.Conclusions: Phamerator represents a useful tool for comparative genomic analysis and comparative representations of bacteriophage genomes.