PhageGT：dsDNA噬菌体基因组末端分析软件

PhageGT: dsDNA phage genome termini analysis software

摘要:

[背景] 随着测序费用的降低，越来越多的科学家选择利用高通量测序技术研究噬菌体的基因组序列。通过对这些基因组数据的分析和研究，一些科学家也开发出了判断dsDNA噬菌体末端序列的方法，但这些方法是基于Linux系统下的命令，并没有在Windows操作系统下的软件。[目的] 在Windows平台下开发一款免费的、可以在高通量测序获得的庞大序列文件中找到dsDNA噬菌体基因组末端序列的软件PhageGT。[方法] 使用Viual Studio 2019开发一个基于对话框的微软基础类库（Microsoft Foundation Classes，MFC）应用程序。软件使用C++语言开发，逐行读取序列文件中的每条Reads，并设计相应的算法进行统计、计算。[结果] 软件PhageGT可在高通量测序文件中提取出不同序列出现的频率、排序，并利用提取序列的最高频率和序列平均频率的比值（R值）判断噬菌体基因组是否存在末端序列。[结论] 软件PhageGT的使用比较方便、简单。软件PhageGT和本文所利用的所有测试数据均可从https://zenodo.org/record/4674231#.YHADb-gzZxc免费获得。

关键词:dsDNA噬菌体;高通量测序;基因组末端;PhageGT

Abstract:

[Background] With the reduction of sequencing costs, more and more scientists have used high-throughput sequencing (HTS) technology to study the genome sequence of phages. Some termini analysis theory or methods were developed by some scientists to determine genomic terminal sequences of dsDNA phages. However, these methods are based on the commands under the Linux system. There is no software under the Windows operating system. [Objective] A free software PhageGT, which can be used in the Windows platform, was developed and can detect details of the genome termini of dsDNA phages genome using HTS Reads data and the complete sequence of phage genome. [Methods] A dialog-based Microsoft foundation classes (MFC) application was developed by Visual Studio 2019 and C++ language. Corresponding algorithms were designed for reading HTS Reads data and calculation. [Results] The frequency of the Reads can be calculated and ranked in descending order. The ratio of the highest frequency of the extracted sequence to the average frequency of the sequence (R) can be calculated. [Conclusion] This software PhageGT is very practical. The software PhageGT and all the test data used in this article can be downloaded for free from the website, https://zenodo.org/record/4543997#.YEhtG50zYhQ.

Key words:dsDNA phage;high-throughput sequencing;genomic termini sequences;PhageGT