Hepatitis B Virus Diversity Research Programme, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg 2193, South Africa.
Virol J. 2013 Feb 23;10:62. doi: 10.1186/1743-422X-10-62.
An online tool, which extracts and summarises nucleotide or amino acid sequence data at specified loci of interest, was developed and tested using the basic core promoter/precore (BCP/PC) region of the hepatitis B virus (HBV). The tool is aimed at researchers without specialist computer skills.
The tool consists of a web-based front-end, with a CGI script, which runs Python code to generate an output web-page. The Python code searches the input sequence data for a specified anchor motif, after which it generates summary tables and graphs of residue and motif distributions.
After the user provides an input file in FASTA format containing aligned sequence data (nucleotides or amino acids) and specifies an anchor motif at a known coordinate, the tool summarizes the nucleotides or amino acids at the specified loci, their frequency and analyzes motif patterns of the loci.The tool can output a graph that displays the frequency of mutations relative to a reference sequence. The tool was used to analyze the BCP/PC region of HBV belonging to subgenotypes A1, A2 and subgenotype D and to serotype HBV. The "Discovery Mode" ignores conserved loci and assists in identifying potential loci of interest.
Although HBV was used to demonstrate the utility of the Mutation Reporter Tool, the tool has wide application as it is genome-agnostic: nucleotide or amino acid sequence data from any organism can be processed. Rapid characterisation of many sequences can be achieved easily when the loci of interest are known. The tool is available online, without charge, at http://hvdr.bioinf.wits.ac.za/tools.
本研究开发并测试了一种在线工具，该工具可提取并总结特定感兴趣区域的核苷酸或氨基酸序列数据，应用对象为乙型肝炎病毒（HBV）的基本核心启动子/前核心（BCP/PC）区域。该工具旨在为不具备专业计算机技能的研究人员服务。
该工具由一个基于网络的前端组成，前端配备一个 CGI 脚本，该脚本运行 Python 代码生成一个输出网页。Python 代码会在输入序列数据中搜索指定的锚定基序，然后生成残基和基序分布的摘要表和图表。
用户提供包含对齐序列数据（核苷酸或氨基酸）的 FASTA 格式输入文件，并在已知坐标处指定锚定基序后，该工具会总结指定位置的核苷酸或氨基酸、它们的频率，并分析该位置的基序模式。该工具可以输出一个图形，显示相对于参考序列的突变频率。该工具用于分析属于 A1、A2 和 D 亚型以及 HBV 血清型的 HBV 的 BCP/PC 区域。“发现模式”忽略保守区域，并有助于确定潜在的感兴趣区域。
虽然 HBV 被用于展示突变报告工具的实用性，但该工具具有广泛的应用，因为它与基因组无关：可以处理任何生物体的核苷酸或氨基酸序列数据。当已知感兴趣的区域时，可以轻松实现对许多序列的快速特征描述。该工具可在线免费使用，网址为 http://hvdr.bioinf.wits.ac.za/tools。
