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Open Access Publications from the University of California

MicrobesOnline: An Integrated Portal For Comparative Functional Genomics (R-018)


The MicrobesOnline database ( currently contains 430 microbial genomes as of our March 2007 release and will soon be expanded to over 600 by Fall 2007. Together with a suite of visualization, analysis, and annotation tools, MicrobesOnline provides a comprehensive framework for studying important comparative and evolutionary genomic questions. MicrobesOnline offers many useful tools including a multi-species genome browser, operon and regulon prediction methods and results, gene ontology browser, capabilities for community annotation of genomes, and a user workbench, which allows users to store arbitrary sets of sequences for further analysis including the ability to generate multiple sequence alignments and custom gene trees. In our most recent software release, we've added a combined gene and species phylogeny browser (see Tree Browser), sequence motif detection and motif search tools in the user workbench, and tools for viewing and mining gene expression microarray, proteomic, and phenotype microarray data (see Expression Profile Searches).

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