1. Solving the protein sequence metric problem
- Author
-
William R. Atchley, Tanja Drüke, Andrew D. Fernandes, and Jieping Zhao
- Subjects
multivariate statistics ,Protein Conformation ,Sequence analysis ,Polarity (physics) ,Static Electricity ,Statistics as Topic ,factor analysis ,Computational biology ,amino acid attributes ,Structural bioinformatics ,Protein sequencing ,Cluster Analysis ,Amino Acid Sequence ,Codon ,Peptide sequence ,Phylogeny ,Mathematics ,Genetics ,chemistry.chemical_classification ,Analysis of Variance ,Multidisciplinary ,Models, Genetic ,molecular evolution ,Computational Biology ,Discriminant Analysis ,Genetic Variation ,Biological Sciences ,Linear discriminant analysis ,Amino acid ,chemistry ,basic helix-loop-helix ,Multivariate Analysis ,Metric (mathematics) - Abstract
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.
- Published
- 2005