Holly McCann, Caeden D Meade, Loren Dean Williams, Anton S Petrov, Philip Z Johnson, Anne E Simon, David Hoksza, Eric P Nawrocki, Patricia P Chan, Todd M Lowe, Carlos Eduardo Ribas, Blake A Sweeney, Fábio Madeira, Stephen Anyango, Sri Devan Appasamy, Mandar Deshpande, Mihaly Varadi, Sameer Velankar, Craig L Zirbel, Aleksei Naiden, Fabrice Jossinet, Anton I Petrov
{"title":"R2DT: RNA二级结构可视化的综合平台。","authors":"Holly McCann, Caeden D Meade, Loren Dean Williams, Anton S Petrov, Philip Z Johnson, Anne E Simon, David Hoksza, Eric P Nawrocki, Patricia P Chan, Todd M Lowe, Carlos Eduardo Ribas, Blake A Sweeney, Fábio Madeira, Stephen Anyango, Sri Devan Appasamy, Mandar Deshpande, Mihaly Varadi, Sameer Velankar, Craig L Zirbel, Aleksei Naiden, Fabrice Jossinet, Anton I Petrov","doi":"10.1093/nar/gkaf032","DOIUrl":null,"url":null,"abstract":"<p><p>RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 4","pages":""},"PeriodicalIF":13.1000,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11806352/pdf/","citationCount":"0","resultStr":"{\"title\":\"R2DT: a comprehensive platform for visualizing RNA secondary structure.\",\"authors\":\"Holly McCann, Caeden D Meade, Loren Dean Williams, Anton S Petrov, Philip Z Johnson, Anne E Simon, David Hoksza, Eric P Nawrocki, Patricia P Chan, Todd M Lowe, Carlos Eduardo Ribas, Blake A Sweeney, Fábio Madeira, Stephen Anyango, Sri Devan Appasamy, Mandar Deshpande, Mihaly Varadi, Sameer Velankar, Craig L Zirbel, Aleksei Naiden, Fabrice Jossinet, Anton I Petrov\",\"doi\":\"10.1093/nar/gkaf032\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio.</p>\",\"PeriodicalId\":19471,\"journal\":{\"name\":\"Nucleic Acids Research\",\"volume\":\"53 4\",\"pages\":\"\"},\"PeriodicalIF\":13.1000,\"publicationDate\":\"2025-02-08\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11806352/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Nucleic Acids Research\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/nar/gkaf032\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Nucleic Acids Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/nar/gkaf032","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
R2DT: a comprehensive platform for visualizing RNA secondary structure.
RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio.
期刊介绍：
Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.
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