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A fast comparative genome browser for diverse bacteria and archaea.
Price, Morgan N; Arkin, Adam P.
Affiliation
  • Price MN; Environmental Genomics and Systems Biology, Lawrence Berkeley National Lab, Berkeley, California, United States of America.
  • Arkin AP; Environmental Genomics and Systems Biology, Lawrence Berkeley National Lab, Berkeley, California, United States of America.
PLoS One ; 19(4): e0301871, 2024.
Article in En | MEDLINE | ID: mdl-38593165
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.
Subject(s)

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Bacteria / Archaea Language: En Journal: PLoS One Journal subject: CIENCIA / MEDICINA Year: 2024 Document type: Article Affiliation country: United States Publication country: EEUU / ESTADOS UNIDOS / ESTADOS UNIDOS DA AMERICA / EUA / UNITED STATES / UNITED STATES OF AMERICA / US / USA

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Bacteria / Archaea Language: En Journal: PLoS One Journal subject: CIENCIA / MEDICINA Year: 2024 Document type: Article Affiliation country: United States Publication country: EEUU / ESTADOS UNIDOS / ESTADOS UNIDOS DA AMERICA / EUA / UNITED STATES / UNITED STATES OF AMERICA / US / USA