Comparative genomics is a powerful way to identify genes conserved among subsets of related pathogens as well as sequences that differentiate strains and species. ERIC has several components that facilitate genome comparisons and classification of relationships between genes within and across genomes.
Multiple genome alignments
Multiple genome alignments are available for each species of enterobacteria represented in ERIC–BRC (Figure 1). These alignments were constructed using a newly released progressive alignment tool, Mauve 2.0 (8,9), that dramatically improves alignment in regions conserved among subsets of genomes, a particularly important feature for recognition of genomic islands. This new version has significantly improved visualization and navigational tools and provides a powerful mechanism for comparative genomics of bacterial genomes.
Genome alignments are currently available for:
- Six complete Escherichia genomes
- Ten complete Escherichia and Shigella genomes
- Five complete Salmonella genomes
- Seven complete Yersinia genomes
Each alignment includes all available complete published genome sequences as of April 2007 with links directly from the graphical gene display to the annotations in ERIC. As new genomes become available, these alignments will be updated. Older versions will be archived and remain available.
Curated ortholog sets
The ERIC–ASAP database maintains curated sets of proteins predicted to be orthologous. Initial sets of orthologs are constructed by analysis of pairwise BLAST searches between genomes. As described in more detail in the ERIC Ortholog SOP, this process is limited to cases where there is a single unambiguous best reciprocal match, and filtered according to empirically selected comparison-specific thresholds for percent identity and proportion of the proteins aligned. This results in a conservative set of predicted orthologs. These sets are augmented and confirmed by manual review and additional processes such as confirmation of co-linearity in genome alignments.
Generic Genome Browser (Gbrowse)
ERIC provides the GBrowse (10) for querying and viewing genomic data and linking to annotations within the database. Users can search for genes across genomes and zoom in or out on genome maps. There are several tracks of annotation data that can be selected to be displayed. We plan to expand the visualizations available through GBrowse to include high-throughput data sets as well as large-scale bioinformatics predictions such as transcriptional units and regulatory protein-binding sites.
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