Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
Bioinformatics. 2023 Aug 1;39(8). doi: 10.1093/bioinformatics/btad528.
Studying the genetic makeup of viruses and phages through genome analysis is crucial for comprehending their function in causing diseases, progressing medicine, tracing their evolutionary history, monitoring the environment, and creating innovative biotechnologies. However, accessing the necessary data can be challenging due to a lack of dedicated comparative genomic tools and viral and phage databases, which are often outdated. Moreover, many wet bench experimentalists may not have the computational proficiency required to manipulate large amounts of genomic data.
We have developed VAPEX (Virus And Phage EXplorer), a web server which is supported by a database and features a user-friendly web interface. This tool enables users to easily perform various genomic analysis queries on all natural viruses and phages that have been fully sequenced and are listed in the NCBI compendium. VAPEX therefore excels in producing visual depictions of fully resolved synteny maps, which is one of its key strengths. VAPEX has the ability to exhibit a vast array of orthologous gene classes simultaneously through the use of symbolic representation. Additionally, VAPEX can fully analyze user-submitted viral and phage genomes, including those that have not yet been annotated.
VAPEX can be accessed from all current web browsers such as Chrome, Firefox, Edge, Safari, and Opera. VAPEX is freely accessible at https://archaea.i2bc.paris-saclay.fr/vapex/.
通过基因组分析研究病毒和噬菌体的遗传组成对于理解它们在引起疾病、推进医学、追踪其进化历史、监测环境和创造创新生物技术方面的功能至关重要。然而，由于缺乏专门的比较基因组工具和病毒和噬菌体数据库，这些数据库通常已经过时，因此访问必要的数据可能具有挑战性。此外，许多湿实验室实验员可能不具备处理大量基因组数据所需的计算能力。
我们开发了 VAPEX（病毒和噬菌体资源管理器），这是一个基于数据库的网络服务器，具有用户友好的网络界面。该工具使用户能够轻松地对所有已完全测序并在 NCBI 汇编中列出的天然病毒和噬菌体执行各种基因组分析查询。因此，VAPEX 擅长生成完全解析的同线性图谱的可视化表示，这是其主要优势之一。VAPEX 能够通过符号表示同时展示大量的同源基因类。此外，VAPEX 可以完全分析用户提交的病毒和噬菌体基因组，包括那些尚未注释的基因组。
VAPEX 可以从所有当前的网络浏览器（如 Chrome、Firefox、Edge、Safari 和 Opera）访问。VAPEX 可在 https://archaea.i2bc.paris-saclay.fr/vapex/ 免费访问。
