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Search for Dispersed Repeats in Bacterial Genomes Using an Iterative Procedure

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dc.contributor.authorKorotkov, E.
dc.contributor.authorSuvorova, Y.
dc.contributor.authorKostenko, D.
dc.contributor.authorKorotkova, M. A.
dc.contributor.authorКороткова, Мария Александровна
dc.date.accessioned2024-12-27T08:29:58Z
dc.date.available2024-12-27T08:29:58Z
dc.date.issued2023
dc.description.abstractWe 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.
dc.identifier.citationSearch 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
dc.identifier.doi10.3390/ijms241310964
dc.identifier.urihttps://www.doi.org/10.3390/ijms241310964
dc.identifier.urihttps://www.scopus.com/record/display.uri?eid=2-s2.0-85164844432&origin=resultslist
dc.identifier.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS_CPL&DestLinkType=FullRecord&UT=WOS:001028344000001
dc.identifier.urihttps://openrepository.mephi.ru/handle/123456789/29097
dc.relation.ispartofInternational Journal of Molecular Sciences
dc.subjectBacterial genome size
dc.subjectDirect repeat
dc.subjectNucleoid
dc.subjectBacterial Genetics
dc.subjectInterspersed repeat
dc.subjectRepeated sequence
dc.subjectInverted repeat
dc.titleSearch for Dispersed Repeats in Bacterial Genomes Using an Iterative Procedure
dc.typeArticle
dspace.entity.typePublication
oaire.citation.issue13
oaire.citation.volume24
relation.isAuthorOfPublication409f2a9c-cb66-4177-bc3c-ed7c1027fe27
relation.isAuthorOfPublication.latestForDiscovery409f2a9c-cb66-4177-bc3c-ed7c1027fe27
relation.isOrgUnitOfPublication010157d0-1f75-46b2-ab5b-712e3424b4f5
relation.isOrgUnitOfPublication.latestForDiscovery010157d0-1f75-46b2-ab5b-712e3424b4f5
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