Most of the programs presented in the earlier chapters, including those in Chapter 14, work on both peptide and nucleotide sequences. There are a few GCG programs, however, that require protein sequences. Method 1, pattern matching, describes how to identify features of unknown sequences based on homology to known proteins. Method 2 handles the analysis of peptides and protein fragments, which might be useful in protein purification, separation, and identification. Method 3 reveals electrostatic properties of proteins by determining a “titration” curve in the denatured state. Method 4 uses various measures to characterize secondary structure features. Method 5, finally, plots three-dimensional structures arising from predictions.