Tytuł
NEW MODELS AND ALGORITHMS FOR RNA PSEUDOKNOT ORDER ASSIGNMENT
Autorzy
[ 1 ] Instytut Chemii Bioorganicznej Polskiej Akademii Nauk, Polska Akademia Nauk | [ P ] pracownik
Dyscyplina naukowa (Ustawa 2.0)
Rok publikacji
2020
Typ artykułu
artykuł naukowy
Język publikacji
angielski
Słowa kluczowe
Streszczenie
EN The pseudoknot is a specific motif of the RNA structure that highly influences the overall shape and stability of a molecule. It occurs when nucleotides of two disjoint single-stranded fragments of the same chain, separated by a helical fragment, interact with each other and form base pairs. Pseudoknots are characterized by great topological diversity, and their systematic description is still a challenge. In our previous work, we have introduced the pseudoknot order a new coefficient representing the topological complexity of the pseudoknotted RNA structure. It is defined as the minimum number of base pair set decompositions, aimed to obtain the unknotted RNA structure. We have suggested how it can be useful in the interpretation and understanding of a hierarchy of RNA folding. However, it is not trivial to unambiguously identify pseudoknots and determine their orders in an RNA structure. Therefore, since the introduction of this coefficient, we have worked on the method to reliably assign pseudoknot orders in correspondence to the mechanisms that control the biological process leading to their formation in the molecule. Here, we introduce a novel graph coloring-based model for the problem of pseudoknot order assignment. We show a specialized heuristic operating on the proposed model and an alternative integer programming algorithm. The performance of both approaches is compared with that of state-of-the-art algorithms which so far have been most efficient in solving the problem in question. We summarize the results of computational experiments that evaluate our new methods in terms of classification quality on a representative data set originating from the non-redundant RNA 3D structure repository.
Strony (od-do)
315 - 324
Typ licencji
CC BY-ND (uznanie autorstwa - bez utworów zależnych)
Wersja tekstu w otwartym dostępie
ostateczna wersja opublikowana
Data udostępnienia
07.2020
Czas udostępnienia publikacji w sposób otwarty
1 miesiąc po opublikowaniu
Punktacja Ministerstwa / czasopismo
100
Punktacja Ministerstwa / czasopismo w ewaluacji 2017-2021
100
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