75-PERCENT ACCURACY IN PROTEIN SECONDARY STRUCTURE PREDICTION

In this study we present an accurate secondary structure prediction pr ocedure by using a query and related sequences, The most novel aspect of our approach is its reliance on local pairwise alignment of the seq uence to be predicted with each related sequence rather than utilizati on of a multiple alignment, The residue-by-residue accuracy of the met hod is 75% in three structural states after jack-knife tests, The gain in prediction accuracy compared with the existing techniques, which a re at best 72%, is achieved by secondary structure propensities based on both local and long-range effects, utilization of similar sequence information in the from of carefully selected pairwise alignment fragm ents, and reliance on a large collection of known protein primary stru ctures, The method is especially appropriate for large-scale sequence analysis efforts such as genome characterization, where precise and si gnificant multiple sequence alignments are not available or achievable . (C) 1997 Wiley-Liss, Inc.