Hydrophobic cluster analysis (HCA) is an efficient method for analysing and comparing the amino acid sequences of proteins. It relies on two-dimensional representations of the sequences presently generated by simple plot programs working on microcomputers. Two interactive programs, MANSEK and SUNHCA, are described here that operate from Vax and Sun workstations respectively. These programs allow the display of several protein sequences in the form of two-dimensional helical plots suitable for HCA. Several tedious, repetitive and time-consuming steps of HCA have been suppressed by implementing several features such as interactive on-screen manipulations (zoom, translations) of the plots and HCA score calculations on segments chosen by the user. Plots on paper can be obtained through hard copies or plotting subroutines.

A BASIC program, HCABAND, is described which is used to convert the linear amino acid sequence of proteins into a word processor-readable file to generate the 2D-helical representation required for hydrophobic cluster analysis. The user can specify the width of the plot and can use the word processor macro-commands to facilitate visual inspection of the plots. The plots can be easily stored on diskettes, mixed with text and printed. HCABAND features are generally applicable and can be implemented on virtually any microcomputer.