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Patterns of hydrophobicity and sequence conservation are widely used to predict secondary structure (see Chapter 1). Whilst the predicted secondary structure cannot contain any more information than is already available in multiple sequences, it seems that this derived information is effective in fold recognition[Taylor & Thornton, 1984,Fischer & Eisenberg, 1996,Defay & Cohen, 1996,Hubbard & Park, 1995,Rice & Eisenberg, 1997,Rost et al., 1997]. This is in spite of only about 70% average accuracy. Furthermore, Russell et al.russell:jmb97 also showed that secondary structure predictions agree for only about 65% of structurally equivalent residues in pairs of remote homologues and analogues. This result is particularly relevant to this work.