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It takes a community to annotate a genome
(7 October 2002)

The initial outcome of a genome sequencing project is a very large number of G, A, T, and C's. Someone has to go through millions of nucleotides and figure out what it all means. The initial pass, by virtual necessity is done by computer, through automated open reading frame detection and provisional assignment of function by sequence similarity to previously annotated open reading frames. For a significant length of time, this is all the annotation there is, and the errors in annotation are sometimes frightful.

Often a group of humans check the provisional annotation, but it is unreasonable to expect any limited number of humans to be sufficiently learned about all aspects of cyanobacterial physiology and molecular biology to rid the provisional annotation of all its errors. The group that stands the best chance to do the job is cyanobacteriologists as a whole, and Minoru Kanehisa (Kyoto U.), Masahiko Ikeuchi (U. Tokyo), and Tatsuo Omata (U. Nagoya) have resolved to enlist that group.

They have developed an interface to enable annotators to add their bit of wisdom to the genes of the completed genomes of three cyanobacteria: Synechocystis PCC 6803, Anabaena PCC 7120, and Thermosynechococcus elongatus BP-1. The sites focusing on each of the three are called SYORF, ANORF and TEORF, respectively. Annotators are free to work on any of the genes in any of the genomes, so genes may acquire several layers of knowledge from different annotators. So, apart from improving the quality of the annotation, the sites promise to provide the cyanobacteriological community with a valuable resource, an encyclopedia of cyanobacterial genes.

Anyone can see the fruits of this labor by going to the GenomeNet Community Databases web site, clicking on your favorite organism, and logging in as guest with a password of guest.Those wishing to join the effort should click on Guidelines at the top of the page for a link to the system administrator and other instructions.