Endhered Patterns in Matchings and RNA

An is a subset of arcs in matchings, such that the corresponding starting points are consecutive, and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations. We focus on the occurrence frequency of such patterns in matchings and native (real-world)...

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Veröffentlicht in:Journal of computational biology Jg. 32; H. 1; S. 28
Hauptverfasser: Biane, Célia, Hampikian, Greg, Kirgizov, Sergey, Nurligareev, Khaydar
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States 01.01.2025
Schlagworte:
Algorithms
Base Pairing - genetics
Computational Biology - methods
Nucleic Acid Conformation
RNA - chemistry
RNA - genetics
secondary structure
pattern
RNA
combinatorics
matching
ISSN:1557-8666, 1557-8666
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Zusammenfassung:An is a subset of arcs in matchings, such that the corresponding starting points are consecutive, and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations. We focus on the occurrence frequency of such patterns in matchings and native (real-world) RNA structures with pseudoknots. We present combinatorial results related to the distribution and asymptotic behavior of the pattern 21, which corresponds to two consecutive base pairs frequently encountered in RNA, and the pattern 12, representing the archetypal minimal pseudoknot. We show that in matchings these two patterns are equidistributed, which is quite different from what we can find in native RNAs. We also examine the distribution of endhered patterns of size 3, showing how the patterns change under the transformation called . Finally, we compute the distributions of endhered patterns of size 2 and 3 in native secondary RNA structures with pseudoknots and discuss possible outcomes of our study.
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
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ISSN:1557-8666
1557-8666
DOI:10.1089/cmb.2024.0658