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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Posted ContentDOI
The Patchy Distribution of Restriction-Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria.
Matthew S. Fullmer,Matthew S. Fullmer,Matthew Ouellette,Artemis S. Louyakis,R. Thane Papke,Johann Peter Gogarten +5 more
TL;DR: A survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria reveals that some orphan DNAmethyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence.
Journal ArticleDOI
Complete Genome Sequence and Methylome Analysis of Deinococcus wulumuqiensis 479.
Alexey Fomenkov,Yvette A. Luyten,Tamas Vincze,Brian P. Anton,Richard J. Roberts,Richard D. Morgan +5 more
TL;DR: Deinococcus wulumuqiensis 479 is the original source strain for the restriction enzyme DrdI and its complete sequence and full methylome were determined using Pacific Biosciences single-molecule real-time (SMRT) sequencing.
Journal ArticleDOI
Complete Genome Sequence and Methylome Analysis of Acinetobacter calcoaceticus 65.
TL;DR: Acinetobacter calcoaceticus 65 is the original source strain for the restriction enzyme Acc65I and its complete sequence and full methylome were determined using single-molecule real-time (SMRT) sequencing.
Journal ArticleDOI
Diagnosing the drug resistance signature in Plasmodium falciparum: a review from contemporary methods to novel approaches
TL;DR: A review of SNP diagnostic tools used in molecular surveillance of Plasmodium falciparum drug resistance in terms of mechanism, reaction modalities, and development with their virtues and shortcomings is presented in this article.
Book ChapterDOI
Significance Score of Motifs in Biological Sequences
TL;DR: In statistical terms, this is equivalent to compute the p-value of observation n in respect with a relevant reference model if X1:l = X1 .
References
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