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

  • Mathematical Methods in Pattern Recognition
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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.

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Authors and Affiliations

  1. Moscow Institute of Physics and Technology, Institutski per 9, Dolgoprudnyi, 141700, Russia

    I. Yu. Torshin

  2. Russian Branch of the Trace Elements Institute for UNESCO, bol. Tishinski per. 26, Moscow, 109652, Russia

    I. Yu. Torshin

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  1. I. Yu. Torshin
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Ivan Yur’evich Torshin. Born 1972, graduated from the Chemistry Department of Moscow State University (MSU) in 1995. Received Candidate’s degree at the Chemistry Department of Moscow State University in 1997. Senior researcher of the Russian Branch of the Institute of Trace Elements for UNESCO, lecturer at Moscow Institute of Physics and Technology (MIPT) and MSU, a member of the Center of Forecasting and Recognition. Author of 84 papers in reference journals in biology, chemistry, medicine, and computer science, including 3 monographs of the series Bioinformatics in the Post-Genomic Era” (Nova Biomedical Publishers, NY, 2006–2009).

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Torshin, I.Y. The study of the solvability of the genome annotation problem on sets of elementary motifs. Pattern Recognit. Image Anal. 21, 652–662 (2011). https://doi.org/10.1134/S1054661811040171

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  • DOI: https://doi.org/10.1134/S1054661811040171

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