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REBASE specifications

Information


Unique identifier OMICS_06233
Name REBASE
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained No
Wikipedia https://en.wikipedia.org/wiki/Rebase_(database)

Maintainer


This tool is not available anymore.

Publications for REBASE

REBASE citations

 (87)
library_books

Comparative genomics of cocci shaped Sporosarcina strains with diverse spatial isolation

2018
BMC Genomics
PMCID: 5930826
PMID: 29716534
DOI: 10.1186/s12864-018-4635-8

[…] used to identify any base modifications by identifying locations of methylation associated with different motifs between all six PacBio sequenced genomes. Additionally, each motif was run through the REBASE database (http://rebase.neb.com/rebase/rebase.html, New England Biolabs) to check if the motifs were associated with any known restriction enzymes and their associated organisms. Only methylati […]

library_books

Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis

2018
Front Microbiol
PMCID: 5859110
PMID: 29593661
DOI: 10.3389/fmicb.2018.00344

[…] replication in a manner similar to that seen in Escherichia coli. Interestingly, only the methylation motif VANDYAGYA could be also identified in the strain Enterococcus faecium isolate 2014-VREF-63 (Rebase ()).In highly clonal species that share the bulk of their genomes (>95%), such as Francisella, subtle changes, especially those that may alter gene expression such as for example methylation, a […]

library_books

Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing

2018
Genes
PMCID: 5867850
PMID: 29495512
DOI: 10.3390/genes9030129

[…] og via blastp. These sequences range from 347 to 415 amino acids in length, which is similar to the 406-amino acid length of HVO_C0040. These sequences are also all annotated as Type II 5mC MTases on REBASE. An amino acid alignment of these homologs () indicates that sequence similarity is shared in many regions of the amino acid sequences. Many of these regions where significant sequence similari […]

library_books

Analyzing AbrB Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2

2018
Front Microbiol
PMCID: 5863516
PMID: 29599755
DOI: 10.3389/fmicb.2018.00307

[…] tings was used, with the assembled genome. Putative restriction modification systems have been identified using the Restriction-ModificationFinder-1.0 server based on the Restriction Enzyme database (REBASE) (). […]

library_books

Function analysis of 5′ UTR of the cellulosomal xyl doc cluster in Clostridium papyrosolvens

2018
Biotechnol Biofuels
PMCID: 5815224
PMID: 29467821
DOI: 10.1186/s13068-018-1040-0

[…] dification (RM) systems and antibiotic sensitivity for C. papyrosolvens were investigated. Six putative RM operons were found by analyzing its genomic sequences (GenBank: ACXX00000000.2) in silico on REBASE (Restriction Enzyme Database) [, ], consisting of three putative methyltransferases (MT, type II) and 3 putative restriction endonuclease (RE, type IV). Through protein BLAST in PubMed (http:// […]

library_books

Culture Facilitated Comparative Genomics of the Facultative Symbiont Hamiltonella defensa

2018
Genome Biol Evol
PMCID: 5841374
PMID: 29452355
DOI: 10.1093/gbe/evy036

[…] (KEGG Orthology And Links Annotation) (). Putative functions of DNA methyltransferases (MTases) and restriction endonucleases (REases) were assessed by BLASTP against the restriction enzyme database (REBASE) (http://rebase.neb.com/rebase/rebase.html). Annotation files corresponding to the above-described annotation pipeline for each strain plus the reannotation of the 5AT strain are available as , […]

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REBASE institution(s)
New England Biolabs, Ipswich, MA, USA
REBASE funding source(s)
REBASE is funded completely by New England Biolabs.

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