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nf-core/蛋白家族:一个可扩展的管道,用于生成蛋白家族

Evangelos Karatzas¹, Martin Beracochea¹, Fotis A Baltoumas²

¹European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.

|January 21, 2026

概括

甲基因组数据分析得到了NF-core/proteinfamily的增强,这是一个可扩展的管道,用于分组未表征的蛋白质并发现新的蛋白质家族. 这个工具有助于理解微生物多样性和蛋白质功能.

科学领域:

生物信息学是一种生物信息学.
计算生物学计算生物学
基因组学就是基因组学.

背景情况:

甲基因组学已经产生了大量的氨基酸序列数据,大大推进了蛋白质功能和进化研究.
一个主要的挑战是大多数这些蛋白质的功能性不定性,这阻碍了全面的分析.
将未描述的序列与已知的序列分组,可以进行注释转移和功能推理.

研究的目的:

开发一个可扩展和开源的计算管道,用于生成和将蛋白质序列分配给蛋白质家族.
为了解决元基因组学数据的激增,并促进未表征蛋白质的功能注释.
提供可参数化的Nextflow管道,用于创建新生的蛋白质家族或将新蛋白质集成到现有的蛋白质中.

主要方法:

开发一个Nextflow管道 (nf-core/proteinfamily) 用于可扩展的蛋白质家族生成和分配.
使用多个序列对齐来检查功能线索的保存残留物.
对管道的计算性能和生物准确性进行基准测试.

主要成果:

nf-core/proteininfamilies管道展示了可扩展的资源使用,大约与输入数据大小线性.
生成的蛋白质家族非常类似于从已建立的数据库中手动策划的家族.
管道有效地将未表征的序列组合在一起,有助于功能注释和发现.

结论:

nf-core/proteininfamilies管道为管理和分析大规模的元基因组蛋白质数据提供了一个有效的解决方案.
它促进了新型蛋白质家族的发现,并增强了未注释序列的功能特征.
该工具支持了解微生物多样性和蛋白质进化方面的进展.

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