Embed-Search-Align: DNA Sequence Alignment using Transformer Models

no code implementations • 20 Sep 2023 • Pavan Holur, K. C. Enevoldsen, Shreyas Rajesh, Lajoyce Mboning, Thalia Georgiou, Louis-S. Bouchard, Matteo Pellegrini, Vwani Roychowdhury

In this framework, a novel encoder model DNA-ESA generates representations of reads and fragments of the reference, which are projected into a shared vector space where the read-fragment distance is used as surrogate for alignment.

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