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Multiple alignment of promoter sequences from the arabidopsis thaliana l. Genome

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dc.contributor.authorKorotkov, E. V.
dc.contributor.authorSuvorova, Y. M.
dc.contributor.authorKostenko, D. O.
dc.contributor.authorKorotkova, M. A.
dc.contributor.authorКороткова, Мария Александровна
dc.date.accessioned2024-11-29T11:16:00Z
dc.date.available2024-11-29T11:16:00Z
dc.date.issued2021
dc.description.abstract© 2021 by the authors. Licensee MDPI, Basel, Switzerland.In this study, we developed a new mathematical method for performing multiple alignment of highly divergent sequences (MAHDS), i.e., sequences that have on average more than 2.5 substitutions per position (x). We generated sets of artificial DNA sequences with x ranging from 0 to 4.4 and applied MAHDS as well as currently used multiple sequence alignment algorithms, including ClustalW, MAFFT, T-Coffee, Kalign, and Muscle to these sets. The results indicated that most of the existing methods could produce statistically significant alignments only for the sets with x < 2.5, whereas MAHDS could operate on sequences with x = 4.4. We also used MAHDS to analyze a set of promoter sequences from the Arabidopsis thaliana genome and discovered many conserved regions upstream of the transcription initiation site (from −499 to +1 bp); a part of the downstream region (from +1 to +70 bp) also significantly contributed to the obtained alignments. The possibilities of applying the newly developed method for the identification of promoter sequences in any genome are discussed. A server for multiple alignment of nucleotide sequences has been created.
dc.format.extentС. 1-21
dc.identifier.citationMultiple alignment of promoter sequences from the arabidopsis thaliana l. Genome / Korotkov, E.V. [et al.] // Genes. - 2021. - 12. - № 2. - P. 1-21. - 10.3390/genes12020135
dc.identifier.doi10.3390/genes12020135
dc.identifier.urihttps://www.doi.org/10.3390/genes12020135
dc.identifier.urihttps://www.scopus.com/record/display.uri?eid=2-s2.0-85099649870&origin=resultslist
dc.identifier.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS_CPL&DestLinkType=FullRecord&UT=WOS:000622566800001
dc.identifier.urihttps://openrepository.mephi.ru/handle/123456789/23605
dc.relation.ispartofGenes
dc.titleMultiple alignment of promoter sequences from the arabidopsis thaliana l. Genome
dc.typeArticle
dspace.entity.typePublication
oaire.citation.issue2
oaire.citation.volume12
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relation.isAuthorOfPublication.latestForDiscovery409f2a9c-cb66-4177-bc3c-ed7c1027fe27
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