REBASE—a database for DNA restriction and modification: enzymes, genes and genomes
TLDR
REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems that contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data.Abstract:
REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. It contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly. Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing. The contents of REBASE may be browsed from the web http://rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email.read more
Citations
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Journal ArticleDOI
Complete Genome Sequencing and Comparative Genomic Analysis of Streptococcus thermophilus CKDB027, a Promising Probiotic Bacterial Strain
Journal ArticleDOI
Extreme C-to-A Hypermutation at a Site of Cytosine-N4 Methylation.
TL;DR: In this article, a Salmonella enterica Type III restriction-modification system that includes a cytosine-N4 methyltransferase caused an enormous increase in the rate of mutation of the methylated cytosines, which occur at the overlined C in the motif CACCGT.
Journal ArticleDOI
Analysis of deoxynucleosides in bacteriophages ϕEF24C and K and the frequency of a specific restriction site in the genomes of members of the bacteriophage subfamily Spounavirinae.
TL;DR: Liquid chromatography/mass spectrometry showed that phages ϕEF24C and K of the subfamily Spounavirinae have unmodified DNA, which classifies them as Twort-like viruses.
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A New Paradigm for Genus Mycobacterium Population Structure
TL;DR: A minimum spanning tree (MST) model of genus Mycobacterium population structure was robust, unambiguous, transparent for alleles, consistent with genotypes and phenotypes, and statistically testable.
Journal ArticleDOI
Nutrient Loading and Viral Memory Drive Accumulation of Restriction Modification Systems in Bloom-Forming Cyanobacteria.
TL;DR: In this paper, the authors used classic resource competition models to explore the hypothesis that nutrient enrichments drive ecological selection for high restriction modification systems due to increased host-phage contact rate.
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