Acceleration of FM-Index Queries Through Prefix-Free Parsing

Authors Aaron Hong, Marco Oliva , Dominik Köppl , Hideo Bannai , Christina Boucher , Travis Gagie

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Author Details

Aaron Hong
  • Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
Marco Oliva
  • Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
Dominik Köppl
  • Institut für Informatik, Univeristät Münster, Germany
Hideo Bannai
  • M&D Data Science Center, Tokyo Medical and Dental University, Japan
Christina Boucher
  • Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
Travis Gagie
  • Faculty of Computer Science, Dalhousie University, Halifax, Canada

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Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, and Travis Gagie. Acceleration of FM-Index Queries Through Prefix-Free Parsing. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 13:1-13:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


FM-indexes are a crucial data structure in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer [Ferragina and Fischer, 2007] observed in 2007 that word-based indexes often use fewer random accesses than character-based indexes, and thus support faster searches. Since DNA lacks natural word-boundaries, however, it is necessary to parse it somehow before applying word-based FM-indexing. Last year, Deng et al. [Deng et al., 2022] proposed parsing genomic data by induced suffix sorting, and showed the resulting word-based FM-indexes support faster counting queries than standard FM-indexes when patterns are a few thousand characters or longer. In this paper we show that using prefix-free parsing - which takes parameters that let us tune the average length of the phrases - instead of induced suffix sorting, gives a significant speedup for patterns of only a few hundred characters. We implement our method and demonstrate it is between 3 and 18 times faster than competing methods on queries to GRCh38. And was consistently faster on queries made to 25,000, 50,000 and 100,000 SARS-CoV-2 genomes. Hence, it is very clear that our method accelerates the performance of count over all state-of-the-art methods with a minor increase in the memory.

Subject Classification

ACM Subject Classification
  • Theory of computation → Pattern matching
  • FM-index
  • pangenomics
  • scalability
  • word-based indexing
  • random access


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