GCG: Displaying Restriction Sites and Possible Translations in a DNA Sequence

As mentioned in Chapter 3 , restriction maps are generated on a computer using programs that match your sequence against a predefined sequence (referred to as “enzymes”). Positive hits are displayed as a function of the sequence coordinate plotted vs the patterns found. In order to view the result with respect to the amino acid sequence (provided that the DNA sequence does have a reading frame), automatic translation can be achieved by using either a standard codon usage table or any other table provided in the correct format. Site-directed mutagenesis can be planned if the reading frame is known by searching for “silent” restriction sites that can be introduced without altering the peptide sequence. In order to restrict the amount of output resulting from the pattern matching calculation, a preselection of patterns (“enzymes”) can be achieved with a variety of options. Furthermore, parts of the target sequence can be easily excluded from the calculation.