Microcomputer Programs for Prediction and Comparative Evaluation of Protein Secondary Structure From Nucleotide Sequence Data: Application to Ribulose-l,5-Bisphosphate Carboxylase Sequences

Abstract

Apple II PASCAL computer programs are described for routine evaluation of protein secondary structures predicted from DNA or amino acid sequence data. The programs predict protein secondary structure using the directional information algorithm of Garnier et al. (1978), and calculate hydrophobicity (Kyte and Doolittle, 1982), hydrophilicity (Hopp and Woods, 1981), hydrophobic moment (Eisenberg et al, 1984b), and secondary structure propensity profiles. The novel feature of these programs is the application of numeric and graphic methods, designed to facilitate detection and characterization of structural similarities/divergences using the aforementioned structural parameters. The use of the programs is demonstrated on a set of sequences from the large and small subunits of ribulose-l,5-bisphosphate carboxylase.