Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F67985556%3A_____%2F23%3A00576660" target="_blank" >RIV/67985556:_____/23:00576660 - isvavai.cz</a>
Alternative codes found
RIV/68378050:_____/23:00576660
Result on the web
<a href="https://genome.cshlp.org/content/33/8/1395" target="_blank" >https://genome.cshlp.org/content/33/8/1395</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1101/gr.277694.123" target="_blank" >10.1101/gr.277694.123</a>
Alternative languages
Result language
angličtina
Original language name
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models
Original language description
A weak palindromic nucleotide motif is the hallmark of retroviral integration site alignments. Given that the majority of target sequences are not palindromic, the current model explains the symmetry by an overlap of the nonpalindromic motif present on one of the half-sites of the sequences. Here, we show that the implementation of multicomponent mixture models allows for different interpretations consistent with the existence of both palindromic and nonpalindromic submotifs in the sets of integration site sequences. We further show that the weak palindromic motifs result from freely combined site-specific submotifs restricted to only a few positions proximal to the site of integration. The submotifs are formed by either palindrome-forming nucleotide preference or nucleotide exclusion. Using the mixture models, we also identify HIV-1-favored palindromic sequences in Alu repeats serving as local hotspots for integration. The application of the novel statistical approach provides deeper insight into the selection of retroviral integration sites and may prove to be a valuable tool in the analysis of any type of DNA motifs.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2023
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Genome Research
ISSN
1088-9051
e-ISSN
1549-5469
Volume of the periodical
33
Issue of the periodical within the volume
8
Country of publishing house
US - UNITED STATES
Number of pages
15
Pages from-to
1395-1408
UT code for WoS article
001077365500001
EID of the result in the Scopus database
2-s2.0-85173558258