ArticlePloS one2024
A fast comparative genome browser for diverse bacteria and archaea.
Article in PloS one, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Characterization of a Heme-Binding Radical SAM Enzyme HemW fromACS bio & med chem Au · 2026Article
- Protein STM3547 From Salmonella typhimurium Is a Phosphofructose Kinase B-Type Enzyme With Ribose Kinase Activity.Molecular microbiology · 2026Article
- A DNA damage-activated kinase phosphorylates a transcriptional repressor to control bacterial immune pathway expression.The EMBO journal · 2026Article
- A Noncontiguous Code for RNA-Guided DNA Recognition Preceded CRISPR.bioRxiv : the preprint server for biology · 2026Article
- ThebioRxiv : the preprint server for biology · 2026Article
- A widespread gut bacterial lineage distinguished by redox metabolism and phage defense.bioRxiv : the preprint server for biology · 2026Article
- Genetic evidence for a periplasmic protein as a third component for a subset of NtrYX family two-component systems.Journal of bacteriology · 2026Article
- A DNA damage-activated kinase controls bacterial immune pathway expression.bioRxiv : the preprint server for biology · 2026Article
- Biosensor-driven strain engineering reveals key cellular processes for maximizing isoprenol production inScience advances · 2025Article
- Enhancing nucleotide sequence representations in genomic analysis with contrastive optimization.Communications biology · 2025Article
- Using Phylogeny and a Conserved Genomic Neighborhood Analysis to Extract and Visualize Gene Sets Involved in Target Gene Function: The Case of [NiFe]-hydrogenase and Succinate Dehydrogenase.Microbes and environments · 2025Article
- Article
- Interactive tools for functional annotation of bacterial genomes.Database : the journal of biological databases and curation · 2024Article
- AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods.Briefings in bioinformatics · 2024Article
- Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families.Microbial genomics · 2024Article
- Beyond Blast: Enabling Microbiologists to Better Extract Literature, Taxonomic Distributions and Gene Neighborhood Information for Protein Families.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
2 authors.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.