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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Microbial Arsenal of Antiviral Defenses. Part II.
TL;DR: A review of strategies employed by microbes to counter phage infection is presented in this article, focusing on adaptive immunity systems, abortive infection mechanisms, defenses associated with mobile genetic elements, and novel systems discovered in recent years through metagenomic mining.
Journal ArticleDOI
Labeling DNA for single-molecule experiments: methods of labeling internal specific sequences on double-stranded DNA
Hagar Zohar,Susan J. Muller +1 more
TL;DR: Intended for non-specialists seeking accessible solutions to DNA labeling challenges, the approaches outlined emphasize simplicity, robustness, suitability for use by non-biologists, and utility in diverse single-molecule experiments.
Journal ArticleDOI
Genome Sequence of the Thermotolerant Foodborne Pathogen Salmonella enterica Serovar Senftenberg ATCC 43845 and Phylogenetic Analysis of Loci Encoding Increased Protein Quality Control Mechanisms
TL;DR: Analysis of a finished-quality genome sequence of an isolate commonly used in heat resistance studies, S. enterica serovar Senftenberg 775W, demonstrated an interesting observation that this strain contains not just one, but two horizontally acquired thermotolerance locus homologs.
Journal ArticleDOI
Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity.
Teng Xu,Song Qin,Hu Yongwu,Zhijian Song,Jianchao Ying,Peizhen Li,Wei Dong,Fangqing Zhao,Huanming Yang,Qiyu Bao +9 more
TL;DR: The nearly complete genome sequence of A. platensis YZ was determined and found to be closely related to palindromes that involved long inverted repeat sequences and the extensively distributed type IIR restriction enzyme in the Arthrospira genome.
Journal ArticleDOI
Comparative genome analysis of the Lactobacillus brevis species
Marine Feyereisen,Jennifer Mahony,Philip Kelleher,Richard J. Roberts,Tadhg O'Sullivan,Jan-Maarten A. Geertman,Douwe van Sinderen +6 more
TL;DR: Comparative genomic analysis highlighted evolution of the taxon allowing niche colonization, notably adaptation to the beer environment, with approximately 50 chromosomal genes acquired by L. brevis beer-spoiler strains representing approximately 2% of their total chromosomal genetic content.
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