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bioRxiv · 10.1101/2024.03.06.583483

Function-Assigned Masked Superstrings as a Versatile and Compact Data Type for ????-Mer Sets

Sladky, O.·Vesely, P.·Brinda, K.
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Abstract

The design of efficient dynamic data structures for large k-mer sets belongs to central challenges of sequence bioinformatics. Recent advances in compact k-mer set representations via Spectrum-Preserving String Sets (SPSS), culminating with the masked superstring framework, have provided data structures of remarkable space efficiency for wide ranges of k-mer sets. However, the possibility to perform set operations with the resulting indexes has remained limited due to the static nature of the underlying compact representations. Here, we develop f-masked superstrings, a concept combining masked superstrings with custom demasking functions f to enable k-mer set operations based on index merging. Combined with the FMSI index for masked superstrings, we obtain a memory-efficient k-mer membership index and compressed dictionary supporting set operations via Burrows-Wheeler Transform merging. The framework provides a promising theoretical solution to a pressing bioinformatics problem and highlights the potential of f-masked superstrings to become an elementary data type for k-mer sets.

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Sladky, O., Vesely, P., Brinda, K.. 2024-03-11. Function-Assigned Masked Superstrings as a Versatile and Compact Data Type for ????-Mer Sets. https://doi.org/10.1101/2024.03.06.583483

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