SeqForge:一个可扩展的基于对齐的搜索,动机检测和跨元基因组数据集的序列策划平台
Elijah R Bring Horvath1, Jaclyn M Winter1
1Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah, 84112, United States.
bioRxiv : the preprint server for biology
|August 20, 2025
概括
SeqForge是一个用于分析大型微生物和基因组数据集的新工具包. 它简化了序列相似性搜索和动机发现,使复杂的基因组探索可供更多的研究人员使用.
科学领域:
- 基因组学
- 生物信息学
- 计算生物学
背景情况:
- 越来越多的微生物和基因组数据需要高效的分析工具.
- 像BLAST+这样的现有方法通常需要定制脚本来进行大规模的比较搜索和功能注释,这给研究人员带来了挑战.
研究的目的:
- 在大型基因组数据集中开发可扩展的模块化工具包 (SeqForge).
- 自动化数据库创建,查询和结果策划,以进行增强的元基因组探索.
主要方法:
- SeqForge是一个命令行工具包,自动化BLAST+数据库操作,并集成氨基酸基因发现.
- 它支持多种输入格式,并行执行,并提供序列/连续提取和结果解析.
- 包括内置的可视化工具和性能分析的基准测试.
主要成果:
- 在大型基因组数据集中自动化复杂的任务,包括BLAST+搜索和图案检测.
- 该工具包展示了密集的模块与适度的内存需求的近线性运行时间缩放.
- 结果被编制成结构化,易于解析的格式,以简化下游分析.
结论:
- SeqForge减少了大规模元基因组数据分析的计算障碍.
- 它使研究人员能够在没有定制脚本的情况下进行人口规模的BLAST搜索和模式检测.
- 这个免费的,独立于平台的工具包适用于各种计算环境.
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