2019, Suvorova, Y. M., Skryabin, K. G., Korotkova, M. A., Korotkov, E. V., Короткова, Мария Александровна, Коротков, Евгений Вадимович

© The Author(s) 2019. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.A new mathematical method for potential reading frameshift detection in protein-coding sequences (cds) was developed. The algorithm is adjusted to the triplet periodicity of each analysed sequence using dynamic programming and a genetic algorithm. This does not require any preliminary training. Using the developed method, cds from the Arabidopsis thaliana genome were analysed. In total, the algorithm found 9,930 sequences containing one or more potential reading frameshift(s). This is ∼21% of all analysed sequences of the genome. The Type I and Type II error rates were estimated as 11% and 30%, respectively. Similar results were obtained for the genomes of Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Rattus norvegicus and Xenopus tropicalis. Also, the developed algorithm was tested on 17 bacterial genomes. We compared our results with the previously obtained data on the search for potential reading frameshifts in these genomes. This study discussed the possibility that the reading frameshift seems like a relatively frequently encountered mutation; and this mutation could participate in the creation of new genes and proteins.

2021, Kamionskya, A. M., Korotkov, E. V., Korotkova, M. A., Коротков, Евгений Вадимович, Короткова, Мария Александровна

© 2021 by the authors. Licensee MDPI, Basel, Switzerland.Currently, there is a lack of bioinformatics approaches to identify highly divergent tandem repeats (TRs) in eukaryotic genomes. Here, we developed a new mathematical method to search for TRs, which uses a novel algorithm for constructing multiple alignments based on the generation of random position weight matrices (RPWMs), and applied it to detect TRs of 2 to 50 nucleotides long in the rice genome. The RPWM method could find highly divergent TRs in the presence of insertions or deletions. Comparison of the RPWM algorithm with the other methods of TR identification showed that RPWM could detect TRs in which the average number of base substitutions per nucleotide (x) was between 1.5 and 3.2, whereas T-REKS and TRF methods could not detect divergent TRs with x > 1.5. Applied to the search of TRs in the rice genome, the RPWM method revealed that TRs occupied 5% of the genome and that most of them were 2 and 3 bases long. Using RPWM, we also revealed the correlation of TRs with dispersed repeats and transposons, suggesting that some transposons originated from TRs. Thus, the novel RPWM algorithm is an effective tool to search for highly divergent TRs in the genomes.

2019, Korotkov, E. V., Korotkova, M. A., Коротков, Евгений Вадимович, Короткова, Мария Александровна

© 2019 Published under licence by IOP Publishing Ltd.A new mathematical method is proposed for constructing multiple alignment of weakly similar amino acid or nucleotide sequences. The method uses a multiple alignment representation in the form of position-weight matrices (PWM) and global dynamic programming. An optimization procedure for PWM is developed with the aim of finding a multiple alignment with maximum statistical significance. The method allows to find multiple alignment of sequences with the number of nucleotide or amino acid substitutions more than 2.5. The developed approach is applied to obtain multiple alignment of promoter sequences of 600 DNA bases length.

2020, Kamionskya, A. M., Korotkova, M. A., Korotkov, E. V., Короткова, Мария Александровна, Коротков, Евгений Вадимович

© Published under licence by IOP Publishing Ltd.A mathematical method for creating classes of promoter sequences has been developed. The method was used to calculate the classes of promoter sequences from the A.thaliana genome. A total of 16 statistically significant classes of promoter sequences were obtained with class sizes ranging from 8,000 to 100 promoters. The classes obtained allow us to identify potential promoter sequences in various genomes with the number of false positives not exceeding 103 per genome.

2021, Rudenko, V., Korotkov, E., Коротков, Евгений Вадимович

© 2021 by the authors. Licensee MDPI, Basel, Switzerland.We report a Method to Search for Highly Divergent Tandem Repeats (MSHDTR) in protein sequences which considers pairwise correlations between adjacent residues. MSHDTR was compared with some previously developed methods for searching for tandem repeats (TRs) in amino acid sequences, such as T-REKS and XSTREAM, which focus on the identification of TRs with significant sequence similarity, whereas MSHDTR detects repeats that significantly diverged during evolution, accumulating deletions, insertions, and substitutions. The application of MSHDTR to a search of the Swiss-Prot databank revealed over 15 thousand TR-containing amino acid sequences that were difficult to find using the other methods. Among the detected TRs, the most representative were those with consensus lengths of two and seven residues; these TRs were subjected to cluster analysis and the classes of patterns were identified. All TRs detected in this study have been combined into a databank accessible over the WWW.