| UniProt: a worldwide hub of protein knowledge | 2018/11/05 | English | 4,656 |
| RNAmmer: consistent and rapid annotation of ribosomal RNA genes | 2007/04/22 | English | 4,632 |
| The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible | 2016/10/18 | English | 4,534 |
| DrugBank 5.0: a major update to the DrugBank database for 2018 | 2017/11/08 | English | 4,488 |
| The carbohydrate-active enzymes database (CAZy) in 2013 | 2013/11/21 | English | 4,394 |
| Deciphering key features in protein structures with the new ENDscript server | 2014/04/21 | English | 4,360 |
| ARB: a software environment for sequence data | 2004/02/23 | English | 4,345 |
| PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences | 2002/01/01 | | 4,286 |
| NCBI prokaryotic genome annotation pipeline | 2016/06/24 | English | 4,243 |
| Pfam: the protein families database | 2013/11/27 | English | 4,231 |
| KEGG as a reference resource for gene and protein annotation | 2015/10/17 | English | 4,167 |
| SWISS-MODEL: an automated protein homology-modeling server | 2003/07/01 | English | 4,089 |
| Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation | 2021/04/22 | English | 4,087 |
| KEGG for linking genomes to life and the environment | 2007/12/23 | English | 4,045 |
| SIFT: predicting amino acid changes that affect protein function | 2003/07/01 | English | 4,005 |
| The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics | 2009/01/01 | English | 3,987 |
| Interactive Tree Of Life (iTOL) v4: recent updates and new developments | 2019/04/01 | English | 3,884 |
| The Pfam protein families database: towards a more sustainable future | 2015/12/15 | English | 3,708 |
| ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins | 2007/05/08 | English | 3,675 |
| MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity | 2012/01/04 | English | 3,645 |
| miRBase: annotating high confidence microRNAs using deep sequencing data | 2013/11/25 | English | 3,625 |
| Multiple sequence alignment with the Clustal series of programs | 2003/07/01 | English | 3,600 |
| UniProt: the universal protein knowledgebase in 2021 | 2020/11/25 | English | 3,592 |
| Summaries of Affymetrix GeneChip probe level data | 2003/02/15 | | 3,587 |
| SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information | 2014/04/29 | English | 3,569 |
| The Ribosomal Database Project: improved alignments and new tools for rRNA analysis | 2009/01/01 | English | 3,568 |
| deepTools2: a next generation web server for deep-sequencing data analysis | 2016/04/13 | English | 3,545 |
| The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets | 2020/11/25 | English | 3,525 |
| Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees | 2016/04/19 | English | 3,514 |
| MAFFT version 5: improvement in accuracy of multiple sequence alignment | 2005/01/19 | English | 3,512 |