The study of the solvability of the genome annotation problem on sets of elementary motifs

Authors:
I. Yu. Torshin
Affiliations:
Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia 141700 and Russian Branch of the Trace Elements Institute for UNESCO, Moscow, Russia 109652
Venue:
Pattern Recognition and Image Analysis
Year:
2011

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Abstract

The problem of genome annotation (i.e., the establishment of the biological roles of proteins and corresponding genes) is one of the major tasks of postgenomic bioinformatics. This paper reports the development of the previously proposed formalism for the study of the local solvability of the genome annotation problem. Here, we introduce the concepts of elementary motifs, positional independence of motifs, heuristic evaluation of informativeness, and solvability on the sets of elementary motifs. We show that introduction of a linear order in a set of elementary motifs allows us to calculate the irreducible motif sets. The formalism was used in experiments to compute the sets of the most informative motifs for several protein functions.