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https://hdl.handle.net/2183/46486 Hybrid MPI/OpenMP Implementation of RIblast for Transcriptome-Scale lncRNA–RNA Interaction Prediction
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Amatria-Barral, I., González-Domínguez, J., Touriño, J. (2026). Hybrid MPI/OpenMP Implementation of RIblast for Transcriptome-Scale lncRNA–RNA Interaction Prediction. In: Hamada, M., Fukunaga, T., Zeng, C. (eds) RNA-RNA and RNA-DNA Interactions. Methods in Molecular Biology, vol 2949. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-4670-0_10
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[Abstract]: Because the identification of RNA interaction partners for each long noncoding RNA (lncRNA) has proven to be a powerful approach for inferring lncRNA functions, numerous tools have been developed to predict lncRNA–RNA interactions. However, their application at the transcriptome scale has been hindered by high computational costs. In this chapter, we introduce pRIblast, a hybrid MPI/OpenMP implementation of the RIblast algorithm designed for large-scale lncRNA–RNA interaction analyses. pRIblast leverages cluster environments and supercomputing facilities to reduce the computational costs of these studies dramatically. Moreover, pRIblast has been thoroughly optimized, and it can take on huge datasets that were impossible to analyze with the former RIblast algorithm.
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This version of the article has been accepted for publication, after peer review (when applicable) and is subject to Springer Nature’s AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at: http://dx.doi.org/10.1007/978-1-0716-4670-0_10
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© 2026 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature