Publication:
Search for Dispersed Repeats in Bacterial Genomes Using an Iterative Procedure

Файлы
W4382752173.pdf(1.69 MB)
Дата
2023
Авторы
Korotkov, E.
Suvorova, Y.
Kostenko, D.
Korotkova, M. A.
Journal Title
Journal ISSN
Volume Title
Издатель
Научные группы
Организационные подразделения
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Организационная единица
Институт интеллектуальных кибернетических систем
Цель ИИКС и стратегия развития - это подготовка кадров, способных противостоять современным угрозам и вызовам, обладающих знаниями и компетенциями в области кибернетики, информационной и финансовой безопасности для решения задач разработки базового программного обеспечения, повышения защищенности критически важных информационных систем и противодействия отмыванию денег, полученных преступным путем, и финансированию терроризма.
Выпуск журнала
Аннотация
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 created algorithm (IP method) allows detection of dispersed repeats for which the average number of substitutions between any two repeats per nucleotide (x) is less than or equal to 1.5. We have shown that all previously developed methods and algorithms (RED, RECON, and some others) can only find dispersed repeats for x ≤ 1.0. We applied the IP method to find dispersed repeats in the genomes of E. coli and nine other bacterial species. We identify three families of approximately 1.09 × 106, 0.64 × 106, and 0.58 × 106 DNA bases, respectively, constituting almost 50% of the complete E. coli genome. The length of the repeats is in the range of 400 to 600 bp. Other analyzed bacterial genomes contain one to three families of dispersed repeats with a total number of 103 to 6 × 103 copies. The existence of such highly divergent repeats could be associated with the presence of a single-type triplet periodicity in various genes or with the packing of bacterial DNA into a nucleoid.
Описание
Ключевые слова
Bacterial genome size , Direct repeat , Nucleoid , Bacterial Genetics , Interspersed repeat , Repeated sequence , Inverted repeat
Цитирование
Search for Dispersed Repeats in Bacterial Genomes Using an Iterative Procedure / Korotkov, E. [et al.] // International Journal of Molecular Sciences. - 2023. - 24. - № 13. - 10.3390/ijms241310964
URI
https://www.doi.org/10.3390/ijms241310964
 https://www.scopus.com/record/display.uri?eid=2-s2.0-85164844432&origin=resultslist
 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS_CPL&DestLinkType=FullRecord&UT=WOS:001028344000001
 https://openrepository.mephi.ru/handle/123456789/29097
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