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
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Posted Content
Misassembly Detection using Paired-End Sequence Reads and Optical Mapping Data
TL;DR: A method called misSEQuel is developed that enhances the quality of draft genomes by identifying misassembly errors and their breakpoints using paired-end sequence reads and optical mapping data and fulfills the critical need for open source computational methods for analyzing optical mappingData.
Journal ArticleDOI
Dormant phages of Helicobacter pylori reveal distinct populations in Europe
Filipa F. Vale,Filipa F. Vale,Filipa F. Vale,J.R. Vadivelu,Mónica Oleastro,Stéphane Breurec,Lars Engstrand,Tsachi Tsadok Perets,Tsachi Tsadok Perets,Francis Mégraud,Francis Mégraud,Philippe Lehours,Philippe Lehours +12 more
TL;DR: It is demonstrated here and for the first time that the diversity of the prophage genes offers the ability to distinguish between European populations, and that H. pylori prophages and their host bacteria share a complex evolutionary history.
Journal ArticleDOI
Intraspecies Genomic Diversity and Long-Term Persistence of Bifidobacterium longum
Andrei V. Chaplin,Boris A. Efimov,Vladimir V. Smeianov,L. I. Kafarskaia,A. P. Pikina,Andrey N. Shkoporov +5 more
TL;DR: The cases of isolation of high genetically similar strains of B. longum from the same patients after long periods of time didn’t succeed in the isolation of genetically identical bacteria: a fact, reflecting the high plasticity of microbiota in children.
Journal ArticleDOI
Origin of the diversity in DNA recognition domains in phasevarion associated modA genes of pathogenic Neisseria and Haemophilus influenzae.
TL;DR: To determine the origin of DRD variability, the 18 modA DRDs were used to search the available databases for similar sequences, and significant matches were identified between several modA alleles and mod gene from distinct bacterial species, indicating one source of theDRD variability was via horizontal gene transfer.
Journal ArticleDOI
Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells
Erik C Hansen,Monica Ransom,Jay R. Hesselberth,Nina N. Hosmane,Adam A. Capoferri,Adam A. Capoferri,Katherine M. Bruner,Ross A. Pollack,Hao Zhang,M.B. Drummond,Janet M. Siliciano,Robert F. Siliciano,Robert F. Siliciano,James T. Stivers +13 more
TL;DR: It is reported that a major subpopulation of monocyte-derived macrophages (MDMs) contains high levels of dUTP, which is incorporated into HIV-1 DNA during reverse transcription (U/A pairs), resulting in pre-integration restriction and post-Integration mutagenesis.
References
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