3plex Web: An interactive platform for RNA:DNA triplex prediction and analysis
Long non-coding RNAs (lncRNAs) exert their functions by cooperating with other molecules, including proteins and DNA. Triplexes, formed through the interaction between a single-stranded RNA (ssRNA) and a double-stranded DNA (dsDNA), have been consistently described as a mechanism that allows lncRNAs...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-01-01
|
| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037025002703 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849430471876804608 |
|---|---|
| author | Marco Masera Chiara Cicconetti Francesca Ferrero Salvatore Oliviero Ivan Molineris |
| author_facet | Marco Masera Chiara Cicconetti Francesca Ferrero Salvatore Oliviero Ivan Molineris |
| author_sort | Marco Masera |
| collection | DOAJ |
| description | Long non-coding RNAs (lncRNAs) exert their functions by cooperating with other molecules, including proteins and DNA. Triplexes, formed through the interaction between a single-stranded RNA (ssRNA) and a double-stranded DNA (dsDNA), have been consistently described as a mechanism that allows lncRNAs to target specific genomic sequences in vivo. Building on the computational tool 3plex, we developed 3plex Web, an accessible platform that enhances the prediction of RNA:DNA triplexes by integrating interactive visualization, statistical evaluation, and user-friendly downstream analysis workflows. 3plex Web implements new features such as input randomization for statistical assessments, interactive profile plotting for triplex stability, and customizable DNA Binding Domain (DBD) selection. This platform enables rapid analysis through PATO, substantially reducing processing times compared to previous methods, while offering Snakemake workflows to integrate gene expression data and explore lncRNA regulatory mechanisms. |
| format | Article |
| id | doaj-art-e4fa489c19a64c78b7e6e41e859b1378 |
| institution | Kabale University |
| issn | 2001-0370 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj-art-e4fa489c19a64c78b7e6e41e859b13782025-08-20T03:27:58ZengElsevierComputational and Structural Biotechnology Journal2001-03702025-01-01273110311310.1016/j.csbj.2025.07.0053plex Web: An interactive platform for RNA:DNA triplex prediction and analysisMarco Masera0Chiara Cicconetti1Francesca Ferrero2Salvatore Oliviero3Ivan Molineris4Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Accademia Albertina 13, Torino, 10126, TO, ItalyDipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Accademia Albertina 13, Torino, 10126, TO, ItalyDipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Accademia Albertina 13, Torino, 10126, TO, ItalyDipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Accademia Albertina 13, Torino, 10126, TO, ItalyCorresponding author.; Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Accademia Albertina 13, Torino, 10126, TO, ItalyLong non-coding RNAs (lncRNAs) exert their functions by cooperating with other molecules, including proteins and DNA. Triplexes, formed through the interaction between a single-stranded RNA (ssRNA) and a double-stranded DNA (dsDNA), have been consistently described as a mechanism that allows lncRNAs to target specific genomic sequences in vivo. Building on the computational tool 3plex, we developed 3plex Web, an accessible platform that enhances the prediction of RNA:DNA triplexes by integrating interactive visualization, statistical evaluation, and user-friendly downstream analysis workflows. 3plex Web implements new features such as input randomization for statistical assessments, interactive profile plotting for triplex stability, and customizable DNA Binding Domain (DBD) selection. This platform enables rapid analysis through PATO, substantially reducing processing times compared to previous methods, while offering Snakemake workflows to integrate gene expression data and explore lncRNA regulatory mechanisms.http://www.sciencedirect.com/science/article/pii/S2001037025002703DNARNARNA–DNA interactionTriplexLong non-coding RNAlncRNA |
| spellingShingle | Marco Masera Chiara Cicconetti Francesca Ferrero Salvatore Oliviero Ivan Molineris 3plex Web: An interactive platform for RNA:DNA triplex prediction and analysis Computational and Structural Biotechnology Journal DNA RNA RNA–DNA interaction Triplex Long non-coding RNA lncRNA |
| title | 3plex Web: An interactive platform for RNA:DNA triplex prediction and analysis |
| title_full | 3plex Web: An interactive platform for RNA:DNA triplex prediction and analysis |
| title_fullStr | 3plex Web: An interactive platform for RNA:DNA triplex prediction and analysis |
| title_full_unstemmed | 3plex Web: An interactive platform for RNA:DNA triplex prediction and analysis |
| title_short | 3plex Web: An interactive platform for RNA:DNA triplex prediction and analysis |
| title_sort | 3plex web an interactive platform for rna dna triplex prediction and analysis |
| topic | DNA RNA RNA–DNA interaction Triplex Long non-coding RNA lncRNA |
| url | http://www.sciencedirect.com/science/article/pii/S2001037025002703 |
| work_keys_str_mv | AT marcomasera 3plexwebaninteractiveplatformforrnadnatriplexpredictionandanalysis AT chiaracicconetti 3plexwebaninteractiveplatformforrnadnatriplexpredictionandanalysis AT francescaferrero 3plexwebaninteractiveplatformforrnadnatriplexpredictionandanalysis AT salvatoreoliviero 3plexwebaninteractiveplatformforrnadnatriplexpredictionandanalysis AT ivanmolineris 3plexwebaninteractiveplatformforrnadnatriplexpredictionandanalysis |