ArticleBMC bioinformatics2002
CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes.
Article in BMC bioinformatics, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- Article
- Characterization and genomic analysis of Cronobacter sakazakii phage JC03, a new member of the genus Pseudotevenvirus.Archives of virology · 2025Article
- New BacteriophageViruses · 2025Article
- Diversity and conservation of the genome architecture of phages infecting the Alphaproteobacteria.Microbiology spectrum · 2024Article
- Characterization of bacteriophage vB_KleM_KB2 possessing high control ability to pathogenic Klebsiella pneumoniae.Scientific reports · 2023Article
- In planta interactions of a novel bacteriophage against Pseudomonas syringae pv. tomato.Applied microbiology and biotechnology · 2023Article
- Comparative genomic analysis of five coprinoid mushrooms species.Functional & integrative genomics · 2023Article
- CoreGenes5.0: An Updated User-Friendly Webserver for the Determination of Core Genes from Sets of Viral and Bacterial Genomes.Viruses · 2022Article
- Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy.Nature communications · 2022Article
- Complete genome sequence analysis and phylogenetic classification of the novel Aeromonas phage AHP-1, a potential member of the genus Tequatrovirus.Archives of virology · 2022Article
- Isolation, Characterization and Draft Genome Analysis of Bacteriophages InfectingFrontiers in microbiology · 2021Article
- Biodiversity of New Lytic Bacteriophages InfectingFrontiers in microbiology · 2021Article
- Characterization of vB_StuS_MMDA13, a Newly Discovered Bacteriophage Infecting the Agar-Degrading SpeciesViruses · 2020Article
- A Tailspike with Exopolysaccharide Depolymerase Activity from a New Providencia stuartii Phage Makes Multidrug-Resistant Bacteria Susceptible to Serum-Mediated Killing.Applied and environmental microbiology · 2020Article
- Article
- Characterization of a newly isolated phage infecting pathogenic Escherichia coli and analysis of its mosaic structural genes.Scientific reports · 2018Article
- Complete Nucleotide Sequence Analysis of a NovelViruses · 2018Article
- Elucidation of the anti-hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis.BMC genomics · 2018Article
- Complete Genome of theFrontiers in microbiology · 2018Article
- Characterization and Genomic Analyses ofFrontiers in microbiology · 2018Article
15 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundImprovements in DNA sequencing technology and methodology have led to the rapid expansion of databases comprising DNA sequence, gene and genome data. Lower operational costs and heightened interest resulting from initial intriguing novel discoveries from genomics are also contributing to the accumulation of these data sets. A major challenge is to analyze and to mine data from these databases, especially whole genomes. There is a need for computational tools that look globally at genomes for data mining.
resultsCoreGenes is a global JAVA-based interactive data mining tool that identifies and catalogs a "core" set of genes from two to five small whole genomes simultaneously. CoreGenes performs hierarchical and iterative BLASTP analyses using one genome as a reference and another as a query. Subsequent query genomes are compared against each newly generated "consensus." These iterations lead to a matrix comprising related genes from this set of genomes, e. g., viruses, mitochondria and chloroplasts. Currently the software is limited to small genomes on the order of 330 kilobases or less.
conclusionA computational tool CoreGenes has been developed to analyze small whole genomes globally. BLAST score-related and putatively essential "core" gene data are displayed as a table with links to GenBank for further data on the genes of interest. This web resource is available at http://pumpkins.ib3.gmu.edu:8080/CoreGenes or http://www.bif.atcc.org/CoreGenes.
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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.