| ExPASy: the proteomics server for in-depth protein knowledge and analysis | 2003/07/01 | English | 3,463 |
| HMMER web server: interactive sequence similarity searching | 2011/05/18 | English | 3,401 |
| Phylogeny.fr: robust phylogenetic analysis for the non-specialist | 2008/05/19 | English | 3,393 |
| KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases | 2011/06/27 | English | 3,319 |
| UniProt: a hub for protein information | 2014/10/27 | English | 3,318 |
| KEGG for integration and interpretation of large-scale molecular data sets | 2011/11/10 | English | 3,317 |
| Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation | 2015/11/08 | English | 3,314 |
| starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data | 2013/12/01 | English | 3,299 |
| The KEGG resource for deciphering the genome | 2004/01/01 | English | 3,255 |
| Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation | 2012/01/28 | English | 3,203 |
| The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) | 2013/11/29 | English | 3,197 |
| KEGG: Kyoto Encyclopedia of Genes and Genomes | 1999/01/01 | English | 3,197 |
| Phytozome: a comparative platform for green plant genomics | 2011/11/22 | English | 3,122 |
| Dali server: conservation mapping in 3D | 2010/05/10 | English | 3,121 |
| tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence | 1997/03/01 | English | 3,089 |
| MolProbity: all-atom contacts and structure validation for proteins and nucleic acids | 2007/05/08 | English | 3,075 |
| High-throughput functional annotation and data mining with the Blast2GO suite | 2008/04/15 | English | 3,072 |
| UniProt: the universal protein knowledgebase | 2016/11/29 | English | 3,048 |
| The Pfam protein families database in 2019 | 2018/10/24 | English | 2,964 |
| The COG database: a tool for genome-scale analysis of protein functions and evolution | 2000/01/01 | | 2,958 |
| The EMBL-EBI search and sequence analysis tools APIs in 2019 | 2019/04/12 | English | 2,950 |
| AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models | 2021/11/17 | English | 2,935 |
| Ribosomal Database Project: data and tools for high throughput rRNA analysis | 2013/11/27 | English | 2,910 |
| STRING v9.1: protein-protein interaction networks, with increased coverage and integration | 2012/11/29 | English | 2,889 |
| PubChem Substance and Compound databases | 2015/09/22 | English | 2,889 |
| KAAS: an automatic genome annotation and pathway reconstruction server | 2007/05/08 | English | 2,888 |
| The Pfam protein families database | 2011/11/29 | English | 2,781 |
| g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) | 2019/05/08 | English | 2,772 |
| The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function | 2010/06/21 | English | 2,687 |
| miRBase: tools for microRNA genomics | 2007/12/23 | English | 2,650 |