ArticleBMC bioinformatics2019
An algebraic language for RNA pseudoknots comparison.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Decoding RNA triple helices: identification from sequence and secondary structure.Briefings in bioinformatics · 2026Article
- Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding.PLoS computational biology · 2024Article
- Automated design of dynamic programming schemes for RNA folding with pseudoknots.Algorithms for molecular biology : AMB · 2023Article
- Automatic generation of pseudoknotted RNAs taxonomy.BMC bioinformatics · 2023Article
- FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures.Biophysical journal · 2022Article
- RNA secondary structure factorization in prime tangles.BMC bioinformatics · 2022Article
- Hierarchical representation for PPI sites prediction.BMC bioinformatics · 2022Article
- Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions.Journal of integrative bioinformatics · 2021Article
- The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes.BMC bioinformatics · 2019Article
- Process calculi may reveal the equivalence lying at the heart of RNA and proteins.Scientific reports · 2019Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA secondary structure comparison is a fundamental task for several studies, among which are RNA structure prediction and evolution. The comparison can currently be done efficiently only for pseudoknot-free structures due to their inherent tree representation.
resultsIn this work, we introduce an algebraic language to represent RNA secondary structures with arbitrary pseudoknots. Each structure is associated with a unique algebraic RNA tree that is derived from a tree grammar having concatenation, nesting and crossing as operators. From an algebraic RNA tree, an abstraction is defined in which the primary structure is neglected. The resulting structural RNA tree allows us to define a new measure of similarity calculated exploiting classical tree alignment.
conclusionsThe tree grammar with its operators permit to uniquely represent any RNA secondary structure as a tree. Structural RNA trees allow us to perform comparison of RNA secondary structures with arbitrary pseudoknots without taking into account the primary structure.
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