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
Using Tablet for visual exploration of second-generation sequencing data
Iain Milne,Gordon Stephen,Micha Bayer,Peter J. A. Cock,Leighton Pritchard,Leighton Pritchard,Linda Cardle,Paul Shaw,A. David Marshall +8 more
TL;DR: This article illustrates how Tablet-a high-performance graphical viewer for visualization of 2GS assemblies and read mappings-plays an important role in the analysis of these data and demonstrates its value in quality assurance and scientific discovery.
Journal ArticleDOI
Nucleases: diversity of structure, function and mechanism
TL;DR: This review surveys nuclease activities with known structures and catalytic machinery and classify them by reaction mechanism and metal-ion dependence and by their biological function ranging from DNA replication, recombination, repair, RNA maturation, processing, interference, to defense, nutrient regeneration or cell death.
Journal ArticleDOI
Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense
TL;DR: New developments which provide insights into the roles of these enzymes in other aspects of cellular function are dealt with, with emphasis placed on novel hypotheses and various findings that have not yet been dealt with in a critical review.
Journal ArticleDOI
The phage-host arms race: Shaping the evolution of microbes
Adi Stern,Rotem Sorek +1 more
TL;DR: The unique and common features of phage resistance mechanisms and their role in global biodiversity are discussed and the commonalities between defense mechanisms suggest avenues for the discovery of novel forms of these mechanisms based on their evolutionary traits.
Journal ArticleDOI
Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
Alicia Mastretta-Yanes,Nils Arrigo,Nadir Alvarez,Tove H. Jorgensen,Daniel Piñero,Brent C. Emerson,Brent C. Emerson +6 more
TL;DR: Individual sample replicates are used, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome and optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci.
References
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Journal ArticleDOI
Host specificity of DNA produced by Escherichia coli. XI. In vitro modification of phage fd replicative form
TL;DR: This activity renders the unmodified replicative form of phage fd resistant to B-specific restriction and is only present in strains carrying intact genes for type B modification.
Journal ArticleDOI
Going beyond five bases in DNA sequencing.
Jonas Korlach,Stephen Turner +1 more
TL;DR: In this opinion, several emerging single-molecule sequencing techniques that have the potential to directly detect many types of DNA modifications as an integral part of the sequencing protocol are highlighted.
Journal ArticleDOI
Using shotgun sequence data to find active restriction enzyme genes
TL;DR: By analyzing shotgun sequence data sets it is shown that this is a reliable method to detect active restriction enzyme genes in newly sequenced genomes, thereby facilitating functional annotation.
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