These programs can find restriction enzyme recognition sites or proteolytic enzyme cut sites in a sequence and display the results in tabular form or with the site locations mapped along the sequence. They can also tell you which enzymes do not cut the sequence, and can find positions in a nucleotide coding sequence where a point mutation could be introduced to add or eliminate a restriction enzyme site without changing the translation. The sites to search for are stored in an external text file; therefore the programs can also be used to search for and display any simple patterns of nucleotides or amino acids if the patterns are placed in a text file of the proper format.

Other programs in this section can predict the fragments resulting from single and double digests. In the case of peptide fragments, the results may also show predicted HPLC retension, composition, and predicted charge of the resulting fragments. There are also programs here that predict the isoelectric point of a protein.

Most of the differences in these programs lie in the options you can use to search for sites and display the results. For example, the GCG Map program allows you to specify the number of mismatches you will allow in performing the search; the EMBOSS digest program allows you to predict fragments resulting from a partial digestion of a protein sequence.

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