[HTML][HTML] Developments in algorithms for sequence alignment: A review

J Chao, F Tang, L Xu - Biomolecules, 2022‏ - mdpi.com
The continuous development of sequencing technologies has enabled researchers to obtain
large amounts of biological sequence data, and this has resulted in increasing demands for …

Study of Dispersed Repeats in the Cyanidioschyzon merolae Genome

V Rudenko, E Korotkov - International Journal of Molecular Sciences, 2024‏ - mdpi.com
In this study, we applied the iterative procedure (IP) method to search for families of highly
diverged dispersed repeats in the genome of Cyanidioschyzon merolae, which contains …

Detection of tandem repeats in the Capsicum annuum genome

V Rudenko, E Korotkov - DNA Research, 2023‏ - academic.oup.com
In this study, we modified the multiple alignment method based on the generation of random
position weight matrices (RPWMs) and used it to search for tandem repeats (TRs) in the …

[HTML][HTML] Application of the MAHDS method for multiple alignment of highly diverged amino acid sequences

DO Kostenko, EV Korotkov - International journal of molecular sciences, 2022‏ - mdpi.com
The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee,
MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly …

[HTML][HTML] Multiple Alignment of Promoter Sequences from the Arabidopsis thaliana L. Genome

EV Korotkov, YM Suvorova, DO Kostenko… - Genes, 2021‏ - mdpi.com
In this study, we developed a new mathematical method for performing multiple alignment of
highly divergent sequences (MAHDS), ie, sequences that have on average more than 2.5 …

Search for dispersed repeats in bacterial genomes using an iterative procedure

E Korotkov, Y Suvorova, D Kostenko… - International Journal of …, 2023‏ - mdpi.com
We have developed a de novo method for the identification of dispersed repeats based on
the use of random position-weight matrices (PWMs) and an iterative procedure (IP). The …

Detection of highly divergent tandem repeats in the rice genome

EV Korotkov, AM Kamionskya, MA Korotkova - Genes, 2021‏ - mdpi.com
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 …

Application of genetic algorithms for periodicity recognition and finite sequences sorting

M Zhassuzak, M Akhmet, Y Amirgaliyev, Z Buribayev - Algorithms, 2024‏ - mdpi.com
Unpredictable strings are sequences of data with complex and erratic behavior, which
makes them an object of interest in various scientific fields. Unpredictable strings related to …

[HTML][HTML] Mathematical Algorithm for Identification of Eukaryotic Promoter Sequences

EV Korotkov, YM Suvorova, AV Nezhdanova… - Symmetry, 2021‏ - mdpi.com
Identification of promoter sequences in the eukaryotic genome, by computer methods, is an
important task of bioinformatics. However, this problem has not been solved since the best …

[HTML][HTML] Classification of promoter sequences from human genome

K Zaytsev, A Fedorov, E Korotkov - International Journal of Molecular …, 2023‏ - mdpi.com
We have developed a new method for promoter sequence classification based on a genetic
algorithm and the MAHDS sequence alignment method. We have created four classes of …