On solvability, regularity, and locality of the problem of genome annotation

Determination of the nucleotide sequences of hundreds of organisms (in the first place, the human genome) is a significant technical achievement of modern biology. The next stage of studying the genome is to determine the functions of each gene and the corresponding protein: the so-called genome annotation. The existing methods of classifying the biological roles of proteins on the basis of the amino acid sequence are restricted to searching for similar sequences in a database and, as a result, have limited applicability. In this paper, a formalism is introduced for studying this problem in the framework of the algebraic approach and the solvability, locality, and regularity of the problem and monotonicity of the condition of solvability are considered. The proposed formalism enables one to study systematically the hypothesis of locality of various biological roles of proteins.