Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments
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DOI：
10.1186/1471-2105-5-96
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发表时间：
2004-07-14
影响因子：
3
通讯作者：
Upton, C
中科院分区：
文献类型：
--
作者：
Brodie, R;Smith, AJ;Upton, C
背景资料：随着越来越多的密切相关的病毒基因组被测序，它已成为理想的是能够比较两个基因组在一个更详细的水平比基因内容，因为两个菌株的生物体可能共享相同的一组预测的基因，但仍然在其致病性谱不同。例如，详细比较天花病毒基因组的多个分离物结果：开发了一个软件包Base-By-Base，它提供了可视化工具，使研究人员能够1）快速识别和纠正大型多基因组比对中的比对错误;以及2）在核苷酸水平上生成基因组之间差异的表格和图形输出。Base-By-Base使用有关比对基因组的详细注释信息，并可以列出具有核苷酸差异的每个预测基因，显示启动子区域或编码区域内是否发生变化以及这些变化是否导致氨基酸取代。Base-By-Base可以连接到我们的mySQL数据库（Virus Orthogonal Clusters; VOC），以检索有关比对基因组的详细注释信息或使用文本文件中的信息。结论：Base-By-Base使用户能够快速轻松地比较大型病毒基因组;它突出了可能导致重要表型差异（如毒力）的微小差异。它可以通过互联网使用Java Web Start，并在Macintosh、PC和带有Java 1.4虚拟机的Linux操作系统上运行。
Background: With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome ( each approximately 200 kb, with 200 genes) is not feasible without new bioinformatics tools.Results: A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1) rapidly identify and correct alignment errors in large, multiple genome alignments; and 2) generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter regions or coding regions and whether these changes result in amino acid substitutions. Base-By-Base can connect to our mySQL database ( Virus Orthologous Clusters; VOCs) to retrieve detailed annotation information about the aligned genomes or use information from text files.Conclusion: Base-By-Base enables users to quickly and easily compare large viral genomes; it highlights small differences that may be responsible for important phenotypic differences such as virulence. It is available via the Internet using Java Web Start and runs on Macintosh, PC and Linux operating systems with the Java 1.4 virtual machine.