Solving the protein sequence metric problem

Biological sequences are composed of long strings of alphabetic letters rather than arrays of numerical values. Lack of a natural underlying metric for comparing such alphabetic data significantly inhibits sophisticated statistical analyses of sequences, modeling structural and functional aspects of proteins, and related problems. Herein, we use multivariate statistical analyses on almost 500 amino acid attributes to produce a small set of highly interpretable numeric patterns of amino acid variability. These high-dimensional attribute data are summarized by five multidimensional patterns of attribute covariation that reflect polarity, secondary structure, molecular volume, codon diversity, and electrostatic charge. Numerical scores for each amino acid then transform amino acid sequences for statistical analyses. Relationships between transformed data and amino acid substitution matrices show significant associations for polarity and codon diversity scores. Transformed alphabetic data are used in analysis of variance and discriminant analysis to study DNA binding in the basic helix-loop-helix proteins. The transformed scores offer a general solution for analyzing a wide variety of sequence analysis problems

Converging Divergence: How Competitive Advantages Condition Institutional Change under EMU

Recognizing that the institutional design of EMU leads to the co-ordination of national wage-bargaining structures, this article asks why bargaining systems in some EMU Member States have become co-ordinated and centralized, whereas others have become co-ordinated and decentralized. In contrast to neoliberal theory, it is argued that different bargaining levels are best explained by a country's competitive advantage: whilst countries with a competitive advantage in high-quality manufacturing favour a centralized bargaining system which supports a high-skill strategy, countries with a competitive advantage in low-cost production prefer decentralized bargaining structures which accommodate high wage differentials within the various employment categories of an industry. Thus, even though EMU asserts unilateral pressure for institutional change, it does not lead to the convergence of national institutions. Copyright Blackwell Publishing Ltd 2005.