ArticleNucleic acids research2001
RNAMotif, an RNA secondary structure definition and search algorithm.
Article in Nucleic acids research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 256 papers.
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Who cites it
256 citing papers in PubMed.
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- High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.bioRxiv : the preprint server for biology · 2025Article
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- Interaction with eukaryotic cells enhances the circularization and transcription of integrative and conjugative elements in Mycoplasma hominis.Mobile DNA · 2025Article
- CHiTA: A scarless high-throughput pipeline for characterization of ribozymes.Methods (San Diego, Calif.) · 2025Article
- Diversity and evolution of viroids and viroid-like agents with circular RNA genomes revealed by metatranscriptome mining.Nucleic acids research · 2025Article
- Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.Nucleic acids research · 2024Article
- Comprehensive Profiling of Roquin Binding Preferences for RNA Stem-Loops.Angewandte Chemie (International ed. in English) · 2024Article
- Transcription termination and antitermination are critical for the fitness and function of the integrative and conjugative element Tn916.PLoS genetics · 2024Article
- Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding.PLoS computational biology · 2024Article
- Surface exclusion of IncC conjugative plasmids and their relatives.PLoS genetics · 2024Article
- Characterization of Mycoviruses inViruses · 2024Article
- Antagonistic interactions between phage and host factors control arbitrium lysis-lysogeny decision.Nature microbiology · 2024Article
- Bacterial small RNAs may mediate immune response differences seen in respiratory syncytial virus versus rhinovirus bronchiolitis.Frontiers in immunology · 2024Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- The NovelViruses · 2023Article
196 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures are assembled from a collection of RNA structural motifs. These basic building blocks are used repeatedly, and in various combinations, to form different RNA types and define their unique structural and functional properties. Identification of recurring RNA structural motifs will therefore enhance our understanding of RNA structure and help associate elements of RNA structure with functional and regulatory elements. Our goal was to develop a computer program that can describe an RNA structural element of any complexity and then search any nucleotide sequence database, including the complete prokaryotic and eukaryotic genomes, for these structural elements. Here we describe in detail a new computational motif search algorithm, RNAMotif, and demonstrate its utility with some motif search examples. RNAMotif differs from other motif search tools in two important aspects: first, the structure definition language is more flexible and can specify any type of base-base interaction; second, RNAMotif provides a user controlled scoring section that can be used to add capabilities that patterns alone cannot provide.
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