Re: Using common protein domains for a faster Human Genome Project?

Dear Bruno,

Your idea about making use of our knowledge of common protein domains to identify genes is a good one, and something that scientists have been doing for some time. Clearly you have some background in molecular biology, so I will refer you to some useful sources of information where you can see how your idea works in action.

You can use the Medline search at PubMed to identify published articles about the use of protein domains to identify gene families (genes which are related evolutionarily and encode proteins with similar functions), receptors with common domains, neuropeptides, signaling molecules, and a host of other genes with common domains. I searched for articles using the key word "common-protein- domains" and got over 2000 references back. I’ve listed three references below which might be of particular interest to you, though you may want to scan the titles at PubMed yourself.

Information about the Human Genome Project can be found at http://www.ornl.gov/TechResources/Human_Genome/home.html. This site contains both scientific updates on progress in the Human Genome Project as well as links to references and tutorials on the goals and methods of the project.

One way that genes are identified which contain common protein domains is by searching databases of sequenced genes and cDNAs (which correspond to messenger RNA, or mRNA created when a gene is expressed). Tools for doing rapid searches for particular protein domains, or conversely, for scanning an unknown gene for similarity to databases of known protein domains, are available from many sites on the Internet. One useful site is Pedro’s Biomolecular Research Tools which has links to many databases and software as well as tutorials and informational sites.

I think you will find something to interest you at these sites. You’re clearly on the right track thinking about how to apply what we know from evolution and protein structure and function to study the human genome in an efficient way.

Best wishes,

Sharon Shriver

Andrade, M.A., and Sander, C. (1997) Bioinformatics: From genome data to 
biological knowledge. Curr Opin Biotechnol 8:675-683.

Ouzounis, C., and Kyrpides, N. (1996) The emergence of major cellular 
processes in evolution. FEBS Lett 390:119-123.