快速而敏感的宏基因组序列分类学分配。

Fast and sensitive taxonomic assignment to metagenomic contigs.

机构信息

Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

School of Biological Sciences, Seoul National University, Seoul, South Korea.

出版信息

Bioinformatics. 2021 Sep 29;37(18):3029-3031. doi: 10.1093/bioinformatics/btab184.

DOI:10.1093/bioinformatics/btab184

PMID:33734313

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8479651/

Abstract

SUMMARY

MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs. It extracts all possible protein fragments from each contig, quickly retains those that can contribute to taxonomic annotation, assigns them with robust labels and determines the contig's taxonomic identity by weighted voting. Its fragment extraction step is suitable for the analysis of all domains of life. MMseqs2 taxonomy is 2-18× faster than state-of-the-art tools and also contains new modules for creating and manipulating taxonomic reference databases as well as reporting and visualizing taxonomic assignments.

AVAILABILITY AND IMPLEMENTATION

MMseqs2 taxonomy is part of the MMseqs2 free open-source software package available for Linux, macOS and Windows at https://mmseqs.com.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

MMseqs2 分类法是一种将分类标签分配给宏基因组序列的新工具。它从每个序列中提取所有可能的蛋白质片段，快速保留那些有助于分类注释的片段，用强大的标签对它们进行分类，并通过加权投票来确定序列的分类身份。其片段提取步骤适用于所有生命领域的分析。MMseqs2 分类法比现有最先进的工具快 2-18 倍，还包含用于创建和操作分类参考数据库以及报告和可视化分类分配的新模块。