| Functional classification | URL | Reference(s) |
| GenProtEC | http://genprotec.mbl.edu/start | Riley, 1998a |
| EcoCyc | http://ecocyc.pangeasystems.com/ | Karp et al., 1999 |
| Sanger Centre (M. tuberculosis) | http://www.sanger.ac.uk/Projects/M_tuberculosis/ | Cole et al., 1998 |
| Institut Pasteur: SubtiList | http://bioweb.pasteur.fr/GenoList/SubtiList/ | Moszer et al., 1996 |
| Institut Pasteur: TubercuList | http://bioweb.pasteur.fr/GenoList/TubercuList/ | Cole et al., 1998 |
| MIPS: Yeast Genome Database (MYGD) | http://www.mips.biochem.mpg.de/proj/yeast/ | Mewes et al., 1997 |
| MIPS: Arabidopsis thaliana Database (MATDB) | http://www.mips.biochem.mpg.de/proj/thal/ | Mewes et al., 1999 |
| MIPS: PEDANT | http://pedant.mips.biochem.mpg.de/ | Frishman and Mewes, 1997 |
| Proteome.com: YDP and WormPD | http://www.proteome.com/databases/index.html | Hodges et al., 1999 |
| MGI: Mouse Genome Database (MGD) | http://www.informatics.jax.org/ | Blake et al., 1999 |
| TIGR: Microbial databases | http://www.tigr.org/tdb/mdb/mdb.html | see TIGR genome papers e.g. Fleischmann et al., 1995 (H. influenzae) Fraser et al., 1995 (M. genitalium) |
| TIGR: Expressed Gene Anatomy Database (EGAD) | http://www.tigr.org/tdb/egad/egad.html | n/a |
| Kyoto Encyclopedia of Genes and Genomes (KEGG) | http://www.genome.ad.jp/kegg/ | Ogata et al., 1999 |
| What Is There (WIT) | http://wit.mcs.anl.gov/WIT2/ | Selkov et al., 1998 |
| COG | http://www.ncbi.nlm.nih.gov/COG | Tatusov et al., 1997 |
| Gene Ontology | http://www.ebi.ac.uk/~ashburn/GO/ http://www.fruitfly.org/~suzi |
Ashburner et al., 1999 other documents available on-line |