REBpredictor

The programs below are designed to help identify the recognition sequences of new restriction enzymes based on the sizes of fragments produced by digesting DNAs of known sequence. The method is published [Gingeras, T.R., Milazzo, J.P. and Roberts, R.J. A computer assisted method for the determination of restriction enzyme recognition sites. Nucleic Acids Res. 5: 4105-4127 (1978)]. Basically it consists of a routine that will take the patterns typically recognized by restriction enzymes and generate a table of all possible digests produced by each example of a pattern. For instance, nnn'n' is a general representation of the 16 tetranucleotide palindromes of the form AATT, ACGT, AGCT, ATAT, CATG etc. The program TABLES (below) will generate all possible digests for a given DNA. The resulting can then be searched by the program PREDICT, which takes as input DNA fragment lengths as estimated from a gel, together with an estimate of the accuracy of that length (+ or a percentage of that length). The output is a list of patterns that satisfy the length criteria. Just keep adding fragment lengths until a unique or manageable number of patterns remains. If no pattern is found, then the restriction enzyme may be recognizing a new kind of pattern or your estimates of sizes are in error. The master tables are stored and additional patterns may be added using the program, UPDATE TABLE.
TABLES

Use this program to compute a new Table for a new DNA sequence.
UPDATE TABLE

Use this program to add a new pattern to the master Tables.
PREDICT

Use this program to search a Table with fragment length data.
Click here to view all patterns currently included.