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
Lowering DNA binding affinity of SssI DNA methyltransferase does not enhance the specificity of targeted DNA methylation in E. coli.
Krystyna Ślaska-Kiss,Nikolett Zsibrita,Nikolett Zsibrita,Mihály Koncz,Mihály Koncz,Pál Albert,Pál Albert,Ákos Csábrádi,Sarolta Szentes,Antal Kiss +9 more
TL;DR: In this paper, the methylation specificity of chimeric MTases containing variants of the CG-specific prokaryotic MTase M.SssI fused to zinc finger or dCas9 targeting domains is influenced by mutations affecting catalytic activity and/or DNA binding affinity of the MTase domain.
Genomic Insights into Campylobacter jejuni Virulence and Population Genetics
TL;DR: An up-to-date review on recent advances in understanding C. jejuni genomics, including structural features of genomes, genetic traits of virulence, population genetics, and epigenetics is provided.
Journal ArticleDOI
Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family.
Giedre Tamulaitiene,Elena Manakova,Virginija Jovaisaite,Gintautas Tamulaitis,Saulius Grazulis,Matthias Bochtler,Matthias Bochtler,Virginijus Siksnys +7 more
TL;DR: Crystal structures of PfoI in free and DNA-bound forms that show unique active site arrangement and mechanism of sequence recognition demonstrate the diversity and versatility of structural mechanisms employed by restriction enzymes for recognition of related DNA sequences.
Journal ArticleDOI
Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses
Nixon Niyonzima,Abigail R. Lambert,Rachel Werther,Harshana S. De Silva Feelixge,Pavitra Roychoudhury,Alexander L. Greninger,Alexander L. Greninger,Daniel Stone,Barry L. Stoddard,Keith R. Jerome,Keith R. Jerome +10 more
TL;DR: The use of yeast surface display and cleavage-dependent flow cytometric assays to increase the specificity of an engineered meganuclease shows a significantly tightened specificity profile, while binding its cognate target site with a slightly lower, but still sub-nanomolar affinity.
Journal ArticleDOI
Methylome Characterization of Burkholderia pseudomallei Strain 982 at Single-Base Resolution.
TL;DR: The complete genome and methylome of melioidosis-causing B. pseudomallei strain 982 is presented and it is shown that methylome dominates in this pathogen.
References
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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.
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