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
Real-Time DNA Sequencing from Single Polymerase Molecules
John Eid,Adrian Fehr,Jeremy Gray,Khai Luong,John Lyle,Geoff Otto,Paul Peluso,David R. Rank,Primo Baybayan,Brad Bettman,Arkadiusz Bibillo,Keith Bjornson,Bidhan Chaudhuri,Fred Christians,Ronald L. Cicero,Sonya Clark,Ravindra V. Dalal,Alex DeWinter,John Dixon,Mathieu Foquet,Alfred Gaertner,Paul Hardenbol,Cheryl Heiner,Kevin Hester,David P. Holden,Gregory J. Kearns,Xiangxu Kong,Ronald Kuse,Yves Lacroix,Steven Lin,Paul Lundquist,Congcong Ma,Patrick Marks,Mark Maxham,Devon Murphy,Insil Park,Thang Pham,Michael Phillips,Joy Roy,Robert Sebra,Gene Shen,Jon M. Sorenson,Austin B. Tomaney,Kevin Travers,Mark Trulson,John Vieceli,Jeffrey Wegener,Dawn Wu,Alicia Yang,Denis Zaccarin,Peter Zhao,Frank Zhong,Jonas Korlach,Stephen Turner +53 more
TL;DR: Single-molecule, real-time sequencing data obtained from a DNA polymerase performing uninterrupted template-directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs) are presented.
Journal ArticleDOI
Direct detection of DNA methylation during single-molecule, real-time sequencing
Benjamin Flusberg,Dale R. Webster,Jessica Lee,Kevin Travers,Eric Olivares,Tyson A. Clark,Jonas Korlach,Stephen Turner +7 more
TL;DR: The direct detection of DNA methylation, without bisulfite conversion, through single-molecule, real-time (SMRT) sequencing is described and is amenable to long read lengths and will likely enable mapping of methylation patterns in even highly repetitive genomic regions.
Book ChapterDOI
Real-time DNA sequencing from single polymerase molecules.
Jonas Korlach,Keith Bjornson,Bidhan Chaudhuri,Ronald L. Cicero,Benjamin Flusberg,Jeremy Gray,David P. Holden,Ravi Saxena,Jeffrey Wegener,Stephen Turner +9 more
TL;DR: This chapter will first outline the principle of this single-molecule, real-time (SMRT) DNA sequencing method, followed by descriptions of its underlying components and typical sequencing run conditions.
Journal ArticleDOI
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
TL;DR: Recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline are reported on.
Journal ArticleDOI
A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes
Richard J. Roberts,Marlene Belfort,Timothy H. Bestor,Ashok S. Bhagwat,Thomas A. Bickle,Jurate Bitinaite,Robert Blumenthal,Sergey Kh. Degtyarev,David T. F. Dryden,Kevin Dybvig,Keith Firman,Elizaveta S. Gromova,Richard I. Gumport,Stephen E. Halford,Stanley Hattman,Joseph Heitman,David P. Hornby,Arvydas Janulaitis,Albert Jeltsch,Jytte Josephsen,Antal Kiss,Todd R. Klaenhammer,Ichizo Kobayashi,Huimin Kong,Detlev H. Krüger,Sanford A. Lacks,Martin G. Marinus,Michiko Miyahara,Richard D. Morgan,Noreen E. Murray,Valakunja Nagaraja,Andrzej Piekarowicz,Alfred Pingoud,Elisabeth A. Raleigh,Desirazu N. Rao,Norbert O. Reich,Repin Vladimir E,Eric U. Selker,Pang-Chui Shaw,Daniel C. Stein,Barry L. Stoddard,Waclaw Szybalski,Thomas A. Trautner,James L. Van Etten,Jorge M. B. Vítor,Geoffrey G. Wilson,Shuang Yong Xu +46 more
TL;DR: In this article, a nomenclature for restriction endonucleases, DNA methyltransferases, homing endon nucleases and related genes and gene products is described.
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