Global Security Computing Applications, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
Biosciences & Biotechnology Research Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
G3 (Bethesda). 2021 May 7;11(5). doi: 10.1093/g3journal/jkab074.
To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations. MultiPhATE2 can be re-started at multiple points within the workflow to allow the user to examine intermediate results and adjust the subsequent computations accordingly. In addition, multiPhATE2 accommodates custom gene calls and sequence databases, again adding flexibility. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC operating systems. Full documentation is provided as a README file and a Wiki website.
为了满足改进噬菌体基因组注释和比较基因组学工具的需求，我们开发了 multiPhATE2。作为之前发布的功能注释代码 multiPhATE 的扩展，multiPhATE2 使用多种算法进行基因预测，比较算法的结果，对编码序列进行功能注释，并整合了额外的搜索算法和数据库来扩展原始代码的搜索空间。multiPhATE2 在一组密切相关的噬菌体基因组之间执行基因匹配，并使用多进程来加速计算。multiPhATE2 可以在工作流程中的多个点重新启动，以允许用户检查中间结果并相应地调整后续计算。此外，multiPhATE2 还可以容纳自定义基因调用和序列数据库，从而增加了灵活性。multiPhATE2 是用 Python 3.7 实现的，并在 Linux 或 MAC 操作系统下作为命令行代码运行。完整的文档作为 README 文件和 Wiki 网站提供。
