167. Annotation of Microbial Genomes 

Frank Larimer, Richard Mural, Morey Parang, Manesh Shah, Victor Olman, Inna Vokler, Jay Snoddy, and Edward C. Uberbacher 
Computational Biosciences, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 
fwl@ornl.gov 
http://compbio.ornl.gov 

Because of their completeness, sequenced microbial genomes present a number of challenges and opportunities not yet fully addressed by genomics. Conventional annotation is inherently single gene-protein centered, yet the operon and regulon organization of microbial genomes immediately accentuates the incompleteness of this simple gene-protein model. Additionally, few attempts have been made to represent regulatory features. Complete genomes require that regulatory and coding elements as well as global and local structural detail be addressed. Although less than a third of the major bacterial taxa have been sampled, a lack of comprehensive tools for representing evolutionary relationships and the richness of microbial diversity is already evident. Finally, the rapid proliferation of completed genomes emphasizes the need for regular updates to annotation. 

We are developing microbial annotation systems to address these needs within the context of the Genome Channel and the Genome Annotation Consortium. In cooperation with The Institute for Genomic Research, we currently have views of the various complete microbial genomes sequenced by TIGR in the Genome Channel. Other complete genomes will be added shortly, and views of genomes in progress will be developed. Among the features being implemented are the following: 

• A visual, integrated contextual browser for viewing genomic relationships from the chromosome to the nucleotide level, within and between genomes;
• Improved and consistent gene calling, with emphasis on accurate prediction of translation start as well as accurate calling of short genes (<300 nt);
• Annotation of structural features, including operon and regulon organization, promoter and ribosome binding site recognition, repressor and activator binding site calling, transcription terminators, and other functional elements; and
• Linkage and integration of the gene/protein/function catalog to phylogenetic, structural, and metabolic relationships.