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
Natural and engineered nicking endonucleases—from cleavage mechanism to engineering of strand-specificity
TL;DR: An overview of the cleavage mechanisms of Types IIS and IIA REases and LAGLIDADG HEases, the engineering of their nicking variants, and the applications of NEases and nicking HEases is provided.
Journal ArticleDOI
A comparative analysis of methylome profiles of Campylobacter jejuni sheep abortion isolate and gastroenteric strains using PacBio data
Kathy T. Mou,Usha Muppirala,Andrew J. Severin,Tyson A. Clark,Matthew Boitano,Paul J. Plummer +5 more
TL;DR: Observations suggest a possible role of methylation in the contrasting disease presentations of these three C. jejuni strains and if variations in methylation patterns could be identified that might explain the role of LuxS-dependent methyl recycling in IA3902 abortifacient potential.
Journal ArticleDOI
iDNA4mC: identifying DNA N4-methylcytosine sites based on nucleotide chemical properties.
TL;DR: The predictive results of the rigorous jackknife test and cross species test demonstrated that the performance of iDNA4mC is quite promising and holds high potential to become a useful tool for identifying 4mC sites.
Journal ArticleDOI
The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts
TL;DR: This work analyzed the distribution of R-M systems in 2261 prokaryote genomes and found their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas systems, integrons and natural transformation.
Journal ArticleDOI
Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks.
TL;DR: The novel results of this study improve the understanding of the genetic mechanisms regulating body growth in ducks and thus provide a genetic basis for breeding programs aimed at maximizing the economic potential of Pekin ducks.
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