the last description of rebase in the 2005 nar database issue ( 1 ) contained more than 3600 biochemically characterized restriction - modification ( rm ) systems and included an analysis of 200 bacterial and archaeal genomes that had been deposited in the refseq database of genbank ( 2 ) . in the interim , the number of sequenced bacterial and archaeal genomes has risen to more than 400 and the total number of rm systems in rebase is now almost 3800 well - characterized systems and more than 4000 systems , whose existence is predicted on the basis of a bioinformatic analysis of dna sequences in genbank . these putative rm genes are named systematically according to recently published nomenclature rules ( 3 ) and all have the suffix the rebase website ( ) summarizes all information known about every restriction enzyme and any associated proteins . this includes the source , commercial availability , sequence data , crystal structure information , cleavage sites , recognition sequences , isoschizomers and methylation sensitivity . within the reference section of rebase , links are maintained to the full text of all papers whenever that is readily available on the web . also , there is extensive reciprocal cross - referencing between rebase and ncbi , including links to genbank and pubmed and ncbi 's linkout utility . links to other major databases such as swiss - prot ( 4 ) , pdb ( 5 ) and pfam ( 6 ) are also maintained . there are currently 3805 biochemically or genetically characterized restriction enzymes in rebase and of the 3698 type ii restriction enzymes , 611 are commercially available , including 262 distinct specificities . as can be seen from figure 1 , the putative restriction and modification enzymes now exceed those for which detailed biochemical characterization is available . however , it should be noted that because of the large number of sequenced examples of biochemically characterized restriction systems , the putative recognition sequences and in some cases the cleavage sites of predicted restriction enzymes can be inferred . these inferences are all included within rebase where they are clearly marked as predictions . among the 2709 restriction enzyme genes and 4485 dna methyltransferase genes that can be identified in genbank , the sequenced microbial genomes the distribution in rebase of the components of the four types of restriction systems is shown . red , restriction enzyme genes ; blue , methyltransferase genes ; and yellow , specificity subunits . full colors indicate genes whose products have been biochemically characterized , whereas shaded areas represent inferred function based on bioinformatic analysis of dna sequences . the pop - out slices ( with numbers in parentheses ) indicate those genes where sequence is available for biochemically characterized enzymes . the identification of putative rm genes in dna sequences is achieved by analyzing each sequence for overall sequence similarity to rebase gene sequences . for dna methyltransferases , which are the primary indicator of an rm system , the presence , proper order and characteristic spacing of well - conserved motifs is used to suggest likely candidates . the more widely divergent genes that encode the restriction enzymes always reside close to the genes for their cognate methyltransferases , but usually they can not be recognized directly because they lack any sequence similarity to any other genes in genbank . given the wealth of experimental data , both published and unpublished , rebase can be a valuable resource during the annotation of bacterial and archaeal genomes . when newly sequenced genes show strong matches to the genes of the type ii restriction systems , their specificity can often be predicted with high accuracy . in particular , because the type ii restriction enzyme genes belong to the category of rapidly evolving genes , strong matches are a particularly good indicator of identical recognition specificity . with the plethora of restriction systems that occur in all sequenced microbial genomes , annotators are encouraged to use the resources of the rebase database or to contact the rebase staff if help is needed . from the rebase website users can use the programs available from the rebase tools icon to analyze dna sequences for the presence of restriction enzyme recognition sites , show all possible restriction patterns of a given dna based on the known enzymes , predict the recognition sequences of an unknown restriction enzyme and additionally , users can keep current with the most recently discovered enzymes and newest references ( news icon ) , browse a variety of useful compilations , including sequence collections and crystal data ( lists icon ) , update the enzyme files being used by software packages such as gcg , dna strider , emboss ( files icon ) and submit new findings for inclusion in rebase ( submit icon ) . the genomes icon leads to a compilation of data for 385 bacterial and 29 archaeal genomes , illustrated by schematic representations of the whole genomes and the individual rm systems within them , providing a quick overview of the rm system content of sequenced genomes . choose the methylation sensitivity icon for all enzymes with methylation sensitivity data , isoschizomers showing differential sensitivity , effects of overlapping methylation and other useful information involving this complex area of study . we offer both simple ( from the home page ) and advanced searching ( search icon ) , where one can search multiple fields , choose result columns and sort order .
rebase is a comprehensive database of information about restriction enzymes , dna methyltransferases and related proteins involved in the biological process of restriction - modification . 
 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 . 
 all newly sequenced genomes are analyzed for the presence of putative restriction systems and these data are included within the rebase . 
 the contents or rebase may be browsed from the web ( ) and selected compilations can be downloaded by ftp ( ) . additionally , monthly updates can be requested via email .