1. Ribosomal proteins
The SWISS-PROT Protein Sequence Data Bank provides under the name RIBOSOMP.TXT a document covering ribosomal proteins classified by families on the basis of sequence similarities. The document aims to provide a common nomenclature for ribosomal proteins, in addition to the previously used names, which are often different in different species; it is distributed with every SWISS-PROT release. It can be found on the web under www.expasy.ch/cgi-bin/lists?ribosomp.txt. The document consists of two parts. The first part is a list of all ribosomal protein families, the name of the PROSITE document for this family and the taxonomic range of this family. The second part lists all SWISS-PROT entries belonging to a given ribosomal protein family.
2. The Gene Family database, GFdb, Mendel-ESTS and Mendel
The rapid expansion of gene sequencing has led to the proliferation of idiosyncratic names for genes, which, even for orthologous sequences, are often inconsistent even between closely related species. The committees encourage examples of good practice in the establishment of gene nomenclature. Examples are set by the "Gene Family database" (Gfdb) and Mendel; databases of gene sequence families and plant gene family nomenclature respectively (http://www.mendel.ac.uk/ & http://genome-www.stanford.edu/Mendel/). All of the 'plant', protist and 'organelle' protein sequences in the SWISS-PROT + TrEMBL protein-sequence databases are assigned a unique accession number which relates them to the sequences in other databases. These sequences are grouped into gene families based on, shared domains, overall sequence similarity and, finally, visual curation. The gene families are assigned a unique gene family number and after checking by experts assigned a Mendel gene family name.
To unify genetic nomenclature among databases a new database Mendel-ESTS has
been created. It cross-references plant EST & STS sequences, in dbEST and dbSTS, to gene families in GFdb and to gene names in Mendel. As a consequence of its central position in plant gene nomenclature and the development of Mendel-ESTS, the Mendel database has been accepted as the authority and reference database for all gene catalogues and plant species databases in the UK and USA. The databases represent a unique resource and can be searched
for most plant sequences, whether by sequence information (DNA or protein), accession number, or text strings that define the gene family.
For further information contact David Lonsdale (Lonsdale@bbsrc.ac.uk)