MicrobesOnline

MicrobesOnline provides comparative and functional analysis of microbial genomes and thousands of expression microarrays across over 1,000 complete bacterial, archaeal, and fungal genomes, including Escherichia coli, Saccharomyces cerevisiae, Desulfovibrio vulgaris, and Shewanella oneidensis, to support evolutionary, regulatory, and metabolic studies.

Key Features:

• Genome collection: Contains over 1,000 complete genomes from bacteria, archaea, and fungi and thousands of expression microarrays.
• Comparative genome browser: Explores gene families using phylogenetic trees and species trees for evolutionary context.
• Phylogenetic analysis: Provides phylogenetic trees and species trees to analyze gene family evolution.
• Expression profile searches: Identifies co-regulated genes by searching and comparing expression microarray profiles.
• Regulatory motif analysis: Detects and analyzes conservation of regulatory motifs across genomes.
• Phylogenetic profile searches: Runs fast phylogenetic profile searches to study gene function and evolutionary relationships.
• Metabolic pathway comparison: Offers comparative views of metabolic pathways across genomes.
• Operon prediction: Predicts operon structure to support regulatory and functional inference.
• Sequence analysis workbench: Provides sequence analysis functions for downstream analyses.
• Resource integration: Integrates with RegTransBase and other microbial genome resources.

Scientific Applications:

• Comparative genomics: Study gene families, orthology, and evolutionary history across bacterial, archaeal, and fungal genomes.
• Gene regulation: Identify co-regulated genes and conserved regulatory motifs to investigate transcriptional regulation.
• Functional inference: Use phylogenetic profile searches and operon predictions to infer gene function and functional linkages.
• Metabolic and physiological analysis: Compare metabolic pathways to investigate microbial physiology and metabolic capabilities.
• Expression analysis: Analyze and compare microarray expression data across model and environmental microbes.

Methodology:

Computational methods explicitly stated include comparative genome browsing, construction and use of phylogenetic trees and species trees, expression profile searches of microarray data, regulatory motif conservation analysis, phylogenetic profile searches, operon prediction, comparative metabolic pathway views, and sequence analysis workbench functions; integration with RegTransBase is also supported.