引用序列浏览器:一个具有用户友好的GUI的R应用程序,可以快速查询序列数据库.
Sriram Ramesh1, Samuel Rapp2, Jorge Tapias Gomez3
1Department of Computer Science and Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America.
PloS one
|October 31, 2024
概括
科学家们开发了参考序列浏览器 (RSB),这是一个简化对环境DNA (eDNA) 分析基因数据库的访问的工具. 该应用程序帮助研究人员有效地找到和下载物种监测的参考序列,而不需要高级计算技能.
科学领域:
- 生态生态学 生态生态学
- 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:
- 环境DNA (eDNA) 对于监测物种多样性和分布至关重要.
- 从多个数据库中识别和访问参考序列是计算密集的.
- 目前的方法需要专门的生物信息技术技能,限制了许多研究人员的可访问性.
研究的目的:
- 开发一种可访问的工具,用于从多个遗传数据库中搜索和检索参考序列.
- 简化eDNA元编码和定量PCR的测试开发过程.
- 为了方便确定目标和非目标类型的参考序列可用性.
主要方法:
- 图形用户界面 (GUI) 的代设计闪亮的应用程序命名为参考序列浏览器 (RSB).
- 整合了来自NCBI核酸,BOLD和CALeDNA CRUX元编码参考数据库的数据.
- 实现搜索过器,包括序列长度和原产国.
主要成果:
- 该RSB提供高效和直观的访问多个遗传数据库.
- 用户可以确定每个生物体的公开可用的条形码标记的数量.
- 该应用程序允许下载FASTA/GenBank文件并探索序列可用性数据.
结论:
- 该RSB民主化了对eDNA研究必不可少的遗传数据的访问.
- 它大大减少了参考序列检索所需的时间和计算专业知识.
- 该工具支持更强大,更有效的物种监测和生物多样性评估.
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