A fast comparative genome browser for diverse bacteria and archaea

Abstract

Genome sequencing has revealed an incredible diversity of bacteria and archaea, but there are no fast and convenient tools for browsing across these genomes. It is cumbersome to view the prevalence of homologs for a protein of interest, or the gene neighborhoods of those homologs, across the diversity of the prokaryotes. We developed a web-based tool, fast.genomics, that uses two strategies to support fast browsing across the diversity of prokaryotes. First, the database of genomes is split up. The main database contains one representative from each of the 6,377 genera that have a high-quality genome, and additional databases for each taxonomic order contain up to 10 representatives of each species. Second, homologs of proteins of interest are identified quickly by using accelerated searches, usually in a few seconds. Once homologs are identified, fast.genomics can quickly show their prevalence across taxa, view their neighboring genes, or compare the prevalence of two different proteins. Fast.genomics is available at https://fast.genomics.lbl.gov.

Interactive Tools for Functional Annotation of Bacterial Genomes

“…To quantify what fraction of bacterial proteins are similar to characterized proteins, we began with a random sample of 2,000 protein-coding genes from diverse bacteria. These were taken from representative genomes in fast.genomics (Price and Arkin 2024) . We compared these proteins to a database of 189,323 experimentally-characterized proteins from all kingdoms of life, which was compiled from ten different databases in the December 2023 release of PaperBLAST (Table 2).…”

“…In particular, genes in conserved operons often have related functions (Dandekar et al 1998; Huynen et al 2000; Wolf et al 2001). The gene neighborhoods of homologs of a protein of interest can be viewed using fast.genomics (http://fast.genomics.lbl.gov/; (Price and Arkin 2024)). A conserved operon will show up as a group of genes that are encoded on the same strand and with a close spacing (usually under 100 nt) across multiple genera (see example in Figure 2B).…”

“…The other fast tools that we are aware of rely on ortholog groups, or pre-computed groups of similar proteins that ideally have the same function. In practice, ortholog groups are often either too broad -- they mix together proteins with different functions -- or too narrow, so that similar proteins that probably have the same function are missing from the group (Price and Arkin 2024). Either way, this can lead to less accurate or confusing results.…”

“…In practice, ortholog groups are often either too broad --they mix together proteins with different functions --or too narrow , so that similar proteins that probably have the same function are missing from the group (Price and Arkin 2024). Either way, this can lead to less accurate or confusing results.…”