title: MicrobesOnline: an integrated portal for comparative and functional genomics.
abstract: Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.
authors.affiliation: Virtual Institute for Microbial Stress and Survival, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. psdehal@lbl.gov
authors.forename: Paramvir S
authors.initials: PS
authors.lastname: Dehal
authors.forename: Marcin P
authors.initials: MP
authors.lastname: Joachimiak
authors.forename: Morgan N
authors.initials: MN
authors.lastname: Price
authors.forename: John T
authors.initials: JT
authors.lastname: Bates
authors.forename: Jason K
authors.initials: JK
authors.lastname: Baumohl
authors.forename: Dylan
authors.initials: D
authors.lastname: Chivian
authors.forename: Greg D
authors.initials: GD
authors.lastname: Friedland
authors.forename: Katherine H
authors.initials: KH
authors.lastname: Huang
authors.forename: Keith
authors.initials: K
authors.lastname: Keller
authors.forename: Pavel S
authors.initials: PS
authors.lastname: Novichkov
authors.forename: Inna L
authors.initials: IL
authors.lastname: Dubchak
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Alm
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics*; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D017434:Protein Structure, Tertiary; D012984:Software