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
More filters
Book ChapterDOI
Host-Mimicking Strategies in DNA Methylation for Improved Bacterial Transformation
TL;DR: Genetic transformation techniques remain important for studying numerous bacteria and for the ad‐ vancement of bacteriology, biochemistry, applied microbiology, and microbial biotechnolo‐ gy.
Posted ContentDOI
Detecting and phasing minor single-nucleotide variants from long-read sequencing data
TL;DR: iGDA, an open-source tool that can accurately detect and phase minor single-nucleotide variants (SNVs), whose frequencies are as low as 0.2%, is introduced, which presents a significant advance towards the complete deciphering of cellular genetic heterogeneity.
Journal ArticleDOI
Complete Genome Sequence of Cupriavidus necator H16 (DSM 428).
Gareth T. Little,Muhammad Ehsaan,Christian Arenas-López,Kamran Jawed,Klaus Winzer,Katalin Kovács,Nigel P. Minton +6 more
TL;DR: The hydrogen-utilizing strain Cupriavidus necator H16 (DSM 428) was sequenced using a combination of PacBio and Illumina sequencing andnotation of this strain reveals 6,543 protein-coding genes, 263 pseudogenes, 64 tRNA genes, and 15 rRNA genes.
Journal ArticleDOI
Beta class amino methyltransferases from bacteria to humans: evolution and structural consequences
TL;DR: It is suggested that M.EcoGII may represent an ancestral form of class beta methyltransferases, as its activity is independent of the nucleic acid type (RNA or DNA), its strandedness (single or double), and its sequence (aside from the target adenine).
Journal ArticleDOI
REBASE: a database for DNA restriction and modification: enzymes, genes and genomes
TL;DR: The database REBASE as discussed by the authors provides information about the recognition and cleavage sites for both restriction enzymes and DNA methyltransferases together with their commercial availability, methylation sensitivity, crystal and sequence data.
References
More filters
Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI
Pfam: the protein families database.
Robert D. Finn,Alex Bateman,Jody Clements,Penelope Coggill,Ruth Y. Eberhardt,Sean R. Eddy,Andreas Heger,Kirstie Hetherington,Liisa Holm,Jaina Mistry,Erik L. L. Sonnhammer,John Tate,Marco Punta +12 more
TL;DR: Pfam as discussed by the authors is a widely used database of protein families, containing 14 831 manually curated entries in the current version, version 27.0, and has been updated several times since 2012.
Journal ArticleDOI
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
TL;DR: The National Center for Biotechnology Information Reference Sequence (RefSeq) database provides a non-redundant collection of sequences representing genomic data, transcripts and proteins that pragmatically includes sequence data that are currently publicly available in the archival databases.
Journal ArticleDOI
Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter,Karin A. Remington,John F. Heidelberg,Aaron L. Halpern,Doug Rusch,Jonathan A. Eisen,Dongying Wu,Ian T. Paulsen,Karen E. Nelson,William C. Nelson,Derrick E. Fouts,Samuel Levy,Anthony H. Knap,Michael W. Lomas,Kenneth H. Nealson,Owen White,Jeremy Peterson,Jeff Hoffman,Rachel Parsons,Holly Baden-Tillson,Cynthia Pfannkoch,Yu-Hui Rogers,Hamilton O. Smith +22 more
TL;DR: Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.
Journal ArticleDOI
The Universal Protein Resource (UniProt)
Amos Marc Bairoch,Rolf Apweiler,Cathy H. Wu,Winona C. Barker,Brigitte Boeckmann,Serenella Ferro,Elisabeth Gasteiger,Hongzhan Huang,Rodrigo Lopez,Michele Magrane,Maria Jesus Martin,Darren A. Natale,Claire O'Donovan,Nicole Redaschi,Lai-Su L. Yeh +14 more
TL;DR: During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; the UniProt keyword list got augmented by additional keywords; the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications.
Related Papers (5)
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
N6-methyl-adenine: an epigenetic signal for DNA-protein interactions.
Didier Wion,Josep Casadesús +1 more