Semantic Analysis for Protein Primary Structure

Abstract

In our everyday life, sentences and words convey meaning behind symbols. In living cells, proteins represent a type of equivalence for sentences and words. In this chapter, we give a semantic analysis for protein sequences in order to explain what protein structures may be telling the cell. Our goals in the semantic analysis of proteins are to find basic words and their meanings, leading to the analysis of the structure of grammar, syntax and semantics. Just as in human languages, there are words in protein sequences. Based on information theory and statistics, we define the local words and give an algorithm to search for them. Using combinatorial graph theory, we describe key words and core words, and analyze their properties. Furthermore, we present search algorithms for key words and core words. These words may play a significant role in protein sequences. Finally, we apply these concepts to the identification of homologous protein structures.