Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies.
Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies.
复制标题
DOI：
10.1186/s12864-016-3018-2
复制
发表时间：
2016-08-26
期刊：
影响因子：
4.4
通讯作者：
Hope S
中科院分区：
文献类型：
--
作者：
Merrill BD;Ward AT;Grose JH;Hope S
噬菌体基因组分析是一个快速发展的领域。经常性的障碍包括软件的访问和可用性，以及在序列方向和/或起始位置上变化的基因组序列。在这里，我们描述修改噬菌体比较基因组学软件程序，Phamerator，提供公众访问的代码，并包括创建自定义Phamerator数据库的说明。我们进一步报告基因组分析技术，以确定噬菌体包装策略和噬菌体基因组的物理末端的识别。原始Phamerator代码可以成功修改，并可以使用我们提供的说明生成自定义数据库。在自定义数据库内的基因组图谱比较的结果揭示了如果已发表的基因组具有不正确的互补性或基因组的第一个碱基的不正确位置，则在执行比较时存在障碍，这是GenBank下载的序列文件中的常见问题。为了解决这些问题，我们回顾了噬菌体包装策略，并提供了使用原始测序数据和软件程序（如PAUSE和Consed）确定基因组物理末端位置的结果，这些结果证明了基因组起始位置和方向的识别。这些结果包括确定确切的直接末端重复序列（DTR）或粘性末端，或是否有可能使用headful包装策略。使用ClustalO和Phamerator中的phamily环的系统发育分析表明，大末端酶基因可用于鉴定噬菌体包装策略，从而有助于鉴定基因组的物理末端。使用可用的在线代码，Phamerator程序可以定制并用于生成具有单独选择的基因组的数据库。然后，这些数据库可以为噬菌体的比较分析提供丰富的信息。研究人员可以使用高通量测序的原始数据结合大末端酶蛋白的系统发育分析和使用定制Phamerator数据库来识别噬菌体基因组的包装策略和物理末端。我们促进出版的噬菌体基因组的方向一致的噬菌体染色体的物理结构，并提供指导，以确定这种结构。本文的在线版本（doi：10.1186/s12864-016-3018-2）包含补充材料，可供授权用户使用。
Phage genome analysis is a rapidly growing field. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation and/or start position. Here we describe modifications to the phage comparative genomics software program, Phamerator, provide public access to the code, and include instructions for creating custom Phamerator databases. We further report genomic analysis techniques to determine phage packaging strategies and identification of the physical ends of phage genomes. The original Phamerator code can be successfully modified and custom databases can be generated using the instructions we provide. Results of genome map comparisons within a custom database reveal obstacles in performing the comparisons if a published genome has an incorrect complementarity or an incorrect location of the first base of the genome, which are common issues in GenBank-downloaded sequence files. To address these issues, we review phage packaging strategies and provide results that demonstrate identification of the genome start location and orientation using raw sequencing data and software programs such as PAUSE and Consed to establish the location of the physical ends of the genome. These results include determination of exact direct terminal repeats (DTRs) or cohesive ends, or whether phages may use a headful packaging strategy. Phylogenetic analysis using ClustalO and phamily circles in Phamerator demonstrate that the large terminase gene can be used to identify the phage packaging strategy and thereby aide in identifying the physical ends of the genome. Using available online code, the Phamerator program can be customized and utilized to generate databases with individually selected genomes. These databases can then provide fruitful information in the comparative analysis of phages. Researchers can identify packaging strategies and physical ends of phage genomes using raw data from high-throughput sequencing in conjunction with phylogenetic analyses of large terminase proteins and the use of custom Phamerator databases. We promote publication of phage genomes in an orientation consistent with the physical structure of the phage chromosome and provide guidance for determining this structure. The online version of this article (doi:10.1186/s12864-016-3018-2) contains supplementary material, which is available to authorized users.
登录
查看更多内容
影响因子：
5.6
作者：
CHUNG, YB;NARDONE, C;HINKLE, DC
通讯作者：
HINKLE, DC
影响因子：
3
作者：
Hauser M;Mayer CE;Söding J
通讯作者：
Söding J
影响因子：
3.7
作者：
CHAI, SH;KRUFT, V;ALONSO, JC
通讯作者：
ALONSO, JC
影响因子：
5.4
作者：
Grose, Julianne H.;Belnap, David M.;Breakwell, Donald P.
通讯作者：
Breakwell, Donald P.
影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.