MANSEK and SUNHCA. Two interactive programs for the hydrophobic cluster analysis of protein sequences

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.