TFinder:用于预测转录因子绑定网站的Python网络工具
Julien Minniti1, Frédéric Checler1, Eric Duplan1
1University Côte d'Azur, INSERM, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, "Laboratory of Excellence (LABEX) Distalz", Valbonne, France.
Journal of molecular biology
|January 22, 2025
概括
TFinder是一个Python网络门户,可以在多种物种的基因调节区域中识别个别动机,如转录因子结合点. 这个工具简化了对缺乏广泛生物信息学经验的研究人员的动机发现.
科学领域:
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
背景情况:
- 转录是调节基因表达的基本细胞过程.
- 转录因子结合位点 (TFBS) 对于特定的DNA结合和基因调节至关重要.
- 识别TFBS对于理解基因控制机制至关重要.
研究的目的:
- 开发一个直观的,全合一的网络门户网站,用于识别个别图案 (IM) 和TFBS.
- 为了促进多种物种的基因调节序列的检索.
- 为了使 de novo生成和利用位置重量矩阵 (PWM) 进行图案分析.
主要方法:
- 使用NCBI API根据基因名称或ID.提取促进子和终端调节区域.
- 使用IUPAC代码和JASPAR条目搜索IM.
- 支持新的PWM生成和现有PWM的使用.
- 同时对五种物种的数据进行无限基因分析.
主要成果:
- TFinder以表格和图形格式提供已识别的图案,包括P值和与转录起始地点 (TSS) 或终端区域相对的位置.
- 结果通过电子邮件发送给用户,方便数据分析和共享.
- 该工具以GitHub上的Python包和Streamlit网络应用程序的形式免费提供.
结论:
- TFinder提供了一个用户友好的解决方案,用于识别基因调节元素和转录因子结合位.
- 它使研究人员,包括那些对生物信息学新手,能够在多种物种中进行复杂的分析.
- 该工具提高了对图案发现的可访问性,有助于随后的数据分析和研究.
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