This page provides information regarding Major Functional Reference Databases for metagenomic data analysis.
| Database | Description | PubMed ID |
|---|---|---|
| UniProtKB | Protein sequence and functional information database, supports taxonomy-based analysis. | 36408920 |
| EggNOG | Functional and phylogenomic annotation of genes, including taxonomic classifications. | 36399505 |
| KEGG | Comprehensive resource for biological pathways and genomes, with taxonomy support. | 36300620 |
| PROKKA Database | Specialized annotation database for bacterial genomes, used in taxonomy assignments. | 24642063 |
| MarFERReT | An open-source, version-controlled reference library of marine microbial eukaryote functional genes. | 38129449 |
| MetaCyc | Database of metabolic pathways and enzymes. | 31586394 |
| CAZy | The carbohydrate-active enzyme database. | 34850161 |
| MEROPS | A database for peptidases and their inhibitors, providing a comprehensive resource for the study of proteolytic enzymes. | 29145643 |
| SEED | A framework for genome annotation, providing curated subsystems and facilitating comparative genomics and metabolic reconstruction. | 24293654 |
| TIGRFAMs | A collection of protein families featuring curated multiple sequence alignments, Hidden Markov Models (HMMs), and associated annotation, useful for protein function prediction. | 23197656 |
| COG (Clusters of Orthologous Groups) | A database of orthologous gene families, facilitating functional annotation of proteins and genome evolution studies. | 39494517 |
| CARD (Comprehensive Antibiotic Resistance Database) | Curated database for AMR genes and associated resistance mechanisms. | 36263822 |
| MEGARes | Provides resistance gene annotations tailored for metagenomic data. | 31722416 |
| VFDB (Virulence Factor Database) | Comprehensive database of virulence factors in bacterial pathogens. | 15608208 |
| MvirDB | Broad repository for virulence and AMR genes, including toxins and pathogenicity islands. | 17090593 |
| PATRIC | Integrative resource for AMR, virulence factors, and pathogen genomes. | 21896772 |
| T3DB (Toxin and Toxin Target Database) | Contains detailed information about toxins, toxicants, and their effects on genes and proteins. | 19897546 |
| ISfinder | A database of bacterial insertion sequences, often linked to resistance gene mobilization. | 16381877 |
| CyanoBase | The genome database for cyanobacteria. | 27899668 |