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bioRxiv · 10.64898/2026.07.31.741718

Fast remote nucleotide sequence alignment with Riboseek

Park, S.·Didi, K.·Favor, A.·Bushuiev, A.·Kim, S.·Mirdita, M.·Steinegger, M.
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Abstract

Structure prediction has reached RNA, where generating deep alignments is now the bottleneck. We developed Riboseek, a search and alignment tool for RNA and DNA that represents sequences as overlapping di-mers. Riboseek is more sensitive for homology detection than BLASTN and nhmmer, and generates alignments 250- and 376-fold faster than nhmmer and rMSA. With structure-aware realignment, it approaches rMSAs base-pair recovery, while remaining 29-fold faster. We provide a web server and 1.7 million precomputed alignments for putatively structured RNAs. Riboseek is freely available at https://github.com/steineggerlab/riboseek.

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Park, S., Didi, K., Favor, A., Bushuiev, A., Kim, S., Mirdita, M., Steinegger, M.. 2026-07-31. Fast remote nucleotide sequence alignment with Riboseek. https://doi.org/10.64898/2026.07.31.741718

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