Table 3.
Databases and methods for the analysis of functional genes from microbial communities
| Type | Name | Description | Website | Ref. |
|---|---|---|---|---|
| Database | ARGminer | Antibiotic resistance gene database | https://bench.cs.vt.edu/argminer | [87] |
| CARD | Comprehensive antibiotic resistance database | https://card.mcmaster.ca/ | [93] | |
| SEED | A database to support effective comparative genome analysis | https://www.theseed.org/wiki/Home_of_the_SEED | [94] | |
| Pfam | A large collection of protein families | https://pfam.xfam.org/ | [95] | |
| EggNOG | A database of orthology relationships, gene evolutionary histories, and functional annotations | https://eggnog5.embl.de/#/app/home | [96] | |
| Uniref | A database provides a comprehensive protein information | https://www.uniprot.org/help/uniref | [97] | |
| MetaCyc | A comprehensive reference database of metabolic pathways and enzymes from all domains of life | https://MetaCyc.org | [98] | |
| KEGG | Kyoto encyclopedia of genes and genomes | https://www.genodme.jp/kegg/ | [99] | |
| Software | DeepARG | A tool with a fully automated data analysis pipeline for antibiotic resistance annotation of raw metagenomic samples | https://bench.cs.vt.edu/deeparg | [43] |
| AntiSMASH | A tool for the rapid genome-wide identification, annotation, and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes | https://antismash.secondarymetabolites.org/ | [42] | |
| HUMAnN2 | A pipeline for profiling the microbial pathways | https://huttenhower.sph.harvard.edu/humann2 | [40] | |
| PICRUSt2 | Provide information about the functional composition of sampled communities | https://github.com/picrust/picrust2 | [100] |