A fast comparative genome browser for diverse bacteria and archaea

Price, Morgan N.; Arkin, Adam P.; Promponas, ed., Vasilis J.

doi:10.1371/journal.pone.0301871

Title: A fast comparative genome browser for diverse bacteria and archaea

Journal Article · 08 April 2024 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0301871 · OSTI ID:2335832

; Arkin, Adam P.; Promponas, ed., Vasilis J.

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 .

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Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2335832

Alternate ID(s):: OSTI ID: 2448507

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 4 Vol. 19; ISSN 1932-6203

Publisher:: Public Library of Science (PLoS)Copyright Statement

Country of Publication:: United States

Language:: English

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