D4 Nucleic Acids Research, 2006, Vol. 34, Database issue the NAR database issues. In the interest of full disclosure, I have cited this Pfam paper myself eight times since its publication in 2004. The second best cited database, Gene Ontology (GO) [http:// www.geneontology.org/, NAR Collection entry no. 487, Ref. (7)] provides structured, controlled vocabularies and classiﬁcations that are also widely used in genome annota- tion, as well as for a variety of bioinformatics tasks. Other databases in the top ﬁve, UniProt [http://www.uniprot.org, NAR Collection entry no. 318, Ref. (8)], SMART [http:// smart.embl.de/, NAR Collection entry no. 218, Ref. (9)] and KEGG [http://www.genome.ad.jp/kegg/, NAR Collection entry no. 112, Ref. (10)], are also used by scientists all over the world. It is worth noting that each of these databases allows free downloading of its full content: they work by adding valuable expertise to the sequence data and have nothing to hide. The databases that form the International Nucleotide Sequence Database Collaboration, NCBI’s GenBank, EMBL Nucleotide database and Japanese DDBJ (NAR Collection entries no. 1–3), also attract a respectable number of citations, even though they are usually mentioned in the literature with- out a formal citation. The same is true for the Protein Data Bank (PDB) (NAR Collection entry no. 276). More databases are probably headed the same way of becoming household names that are not considered to need a citation. On the other side of the spectrum are the databases that have never been cited in these 2 years, even by their own authors. This does not mean, of course, that these databases do not offer a useful content but one could always suggest a reason why nobody has used this or that database. Usually these databases were too speciﬁc in scope and offered content that could be easily found elsewhere. For example, TopoSNP [http://gila-fw.bioengr.uic.edu/snp/toposnp/, NAR Collection entry no. 590, Ref. (11)], maps single nucleotide polymorph- isms onto known protein structures, allowing one to trace the location of the affected amino acid residues and correlate it with disease phenotypes. However, most of its data are extracted from OMIM (http://www.ncbi.nlm.nih.gov/omim/, NAR Collection entry no. 143), which is where the user would probably go ﬁrst. VirGen [http://bioinfo.ernet.in/ virgen/virgen.html, NAR Collection entry no. 397, Ref. (12)] is a database of complete genome sequences of plant and animal viruses. However, it often takes a while for the server to produce a response, which contains little information that would not be available in other databases, such as VIPERdb [http://viperdb.scripps.edu/, NAR Collection entry no. 761, Ref. (13)], Viral Bioinformatics Resource Center (http:// www.virology.ca/, NAR Collection entry no. 798), VIDA (http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA. html, NAR Collection entry no. 201) or the NCBI Viral Genomes (http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/ viruses.html, NAR Collection entry no. 602). The Ribosomal Protein Gene database (RPG) [http://ribosome.miyazaki-med. ac.jp/, NAR Collection entry no. 573, Ref. (14)] lists ribosomal proteins from just a handful of organisms, offering a tiny fraction of information that is available through Pfam, UniProt, KEGG orthology groups and a variety of other sources. The same problem plagues EyeSite, a database of protein families in the eye [http://eyesite.cryst.bbk.ac.uk/, NAR Collection entry no. 464, Ref. (15)]. Even the terriﬁc graphics on its front page cannot compensate for the fact that researchers interested in eye proteins can get their sequences from UniProt and other sequence databases and their structures from PDB. Finally the Signal Transduction Classiﬁcation Database (STCDB) [http://bibiserv.techfak.uni-bielefeld.de/ stcdb/, NAR Collection entry no. 395, Ref. (16)] offers an interesting approach to the hierarchical classiﬁcation of euka- ryotic signaling proteins. However, so many people use the GO classiﬁcation that it has become de facto standard and nobody is looking for alternative classiﬁcation schemes. Thus, the fact that this comment will most probably be the ﬁrst time in 2 years that TopoSNP, VirGen, RPG, EyeSite or STCDB are mentioned in the literature could be a direct consequence of the overwhelming success of other databases. It is an open global marketplace of ideas, tools and approaches; fortunately, nobody goes out of business. Suggestions for the inclusion of additional databases in this Collection should be directed to the author at galperin@ ncbi.nlm.nih.gov. SUPPLEMENTARY DATA Supplementary Data are available at NAR Online. 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