PATO: genome-wide prediction of lncRNA-DNA triple helices
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PATO: genome-wide prediction of lncRNA-DNA triple helicesData
2023-03Cita bibliográfica
Iñaki Amatria-Barral, Jorge González-Domínguez, Juan Touriño, PATO: genome-wide prediction of lncRNA–DNA triple helices, Bioinformatics, Volume 39, Issue 3, March 2023, btad134, https://doi.org/10.1093/bioinformatics/btad134
Resumo
[Abstract]: Motivation: Long non-coding RNA (lncRNA) plays a key role in many biological processes. For instance, lncRNA regulates chromatin using different molecular mechanisms, including direct RNA-DNA hybridization via triplexes, cotranscriptional RNA-RNA interactions, and RNA-DNA binding mediated by protein complexes. While the functional annotation of lncRNA transcripts has been widely studied over the last 20 years, barely a handful of tools have been developed with the specific purpose of detecting and evaluating lncRNA-DNA triple helices. What is worse, some of these tools have nearly grown a decade old, making new triplex-centric pipelines depend on legacy software that cannot thoroughly process all the data made available by next-generation sequencing (NGS) technologies.
Results: We present PATO, a modern, fast, and efficient tool for the detection of lncRNA-DNA triplexes that matches NGS processing capabilities. PATO enables the prediction of triple helices at the genome scale and can process in as little as 1 h more than 60 GB of sequence data using a two-socket server. Moreover, PATO's efficiency allows a more exhaustive search of the triplex-forming solution space, and so PATO achieves higher levels of prediction accuracy in far less time than other tools in the state of the art.
Availability and implementation: Source code, user manual, and tests are freely available to download under the MIT License at https://github.com/UDC-GAC/pato.
Palabras chave
DNA / metabolism
RNA, Long Noncoding* / genetics
RNA, Long Noncoding* / metabolism
Software
RNA, Long Noncoding* / genetics
RNA, Long Noncoding* / metabolism
Software
Versión do editor
Dereitos
Atribución 3.0 España
ISSN
1367-4811