ArticleBMC bioinformatics2020
ElTetrado: a tool for identification and classification of tetrads and quadruplexes.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.Computational and structural biotechnology journal · 2026Article
- Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life.Genome research · 2025Article
- Detecting polynucleotide motifs: Pentads, hexads, and beyond.PLoS computational biology · 2025Article
- WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures.Nucleic acids research · 2023Article
- ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes.Nucleic acids research · 2023Article
- Structural and Functional Classification of G-Quadruplex Families within the Human Genome.Genes · 2023Article
- Contact networks in RNA: a structural bioinformatics study with a new tool.Journal of computer-aided molecular design · 2022Article
- ONQUADRO: a database of experimentally determined quadruplex structures.Nucleic acids research · 2022Article
- Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures.International journal of molecular sciences · 2021Review
- How bioinformatics resources work with G4 RNAs.Briefings in bioinformatics · 2021Review
- DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL.Nucleic acids research · 2020Article
- Topology-based classification of tetrads and quadruplex structures.Bioinformatics (Oxford, England) · 2020Article
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3 authors.
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Abstract
backgroundQuadruplexes are specific structure motifs occurring, e.g., in telomeres and transcriptional regulatory regions. Recent discoveries confirmed their importance in biomedicine and led to an intensified examination of their properties. So far, the study of these motifs has focused mainly on the sequence and the tertiary structure, and concerned canonical structures only. Whereas, more and more non-canonical quadruplex motifs are being discovered.
resultsHere, we present ElTetrado, a software that identifies quadruplexes (composed of guanine- and other nucleobase-containing tetrads) in nucleic acid structures and classifies them according to the recently introduced ONZ taxonomy. The categorization is based on the secondary structure topology of quadruplexes and their component tetrads. It supports the analysis of canonical and non-canonical motifs. Besides the class recognition, ElTetrado prepares a dot-bracket and graphical representations of the secondary structure, which reflect the specificity of the quadruplex's structure topology. It is implemented as a freely available, standalone application, available at https://github.com/tzok/eltetrado.
conclusionsThe proposed software tool allows to identify and classify tetrads and quadruplexes based on the topology of their secondary structures. It complements existing approaches focusing on the sequence and 3D structure.
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