INRAE, Université de Tours, ISP, Nouzilly F-37380, France.
Bioinformatics. 2024 Jun 3;40(6). doi: 10.1093/bioinformatics/btae372.
Understanding the molecular evolutionary history of organisms usually requires visual comparison of genomic regions from related species or strains. Although several applications already exist to achieve this task, they are either too old, too limited, or too complex for most user's needs.
GenoFig is a graphical application for the visualization of prokaryotic genomic regions, intended to be as easy to use as possible and flexible enough to adapt to a variety of needs. GenoFig allows the personalized representation of annotations extracted from GenBank files in a consistent way across sequences, using regular expressions. It also provides several unique options to optimize the display of homologous regions between sequences, as well as other more classical features such as sequence GC percent or GC-skew representations. In summary, GenoFig is a simple, free, and highly configurable tool to explore the evolution of specific genomic regions in prokaryotes and to produce publication-ready figures.
Genofig is fully available at https://forgemia.inra.fr/public-pgba/genofig under a GPL 3.0 license.
理解生物的分子进化历史通常需要对相关物种或菌株的基因组区域进行视觉比较。虽然已经有几个应用程序可以实现此任务，但它们要么太旧、功能太有限，要么对大多数用户的需求来说过于复杂。
GenoFig 是一个用于可视化原核基因组区域的图形应用程序，旨在尽可能易于使用，并具有足够的灵活性以适应各种需求。GenoFig 使用正则表达式，允许以一致的方式在序列中个性化表示从 GenBank 文件中提取的注释。它还提供了一些独特的选项，可优化序列之间同源区域的显示，以及其他更经典的功能，如序列 GC 百分比或 GC 倾斜表示。总之，GenoFig 是一个简单、免费且高度可配置的工具，用于探索原核生物特定基因组区域的进化，并生成可发布的图形。
GenoFig 可在 https://forgemia.inra.fr/public-pgba/genofig 上完全获得，根据 GPL 3.0 许可证提供。
