REBASE--a database for DNA restriction and modification: enzymes, genes and genomes

Abstract

REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. Experimentally characterized homing endonucleases are also included. The fastest growing segment of REBASE contains the putative R-M systems found in the sequence databases. Comprehensive descriptions of the R-M content of all fully sequenced genomes are available including summary schematics. 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). Additionally, monthly updates can be requested via email.

Figure 1.

The graph shows the numbers of R–M systems entering REBASE since its inception in 1975. The open bars show systems that have been characterized either biochemically or genetically. The black bars show the increasing accumulation of potential R–M systems that have been found by bioinformatic analysis of sequences in GenBank. The surge in 2004 represents the addition of metagenomic sequences from the Sargasso Sea collecting expedition (9).