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On the Construction of Elastic Degenerate Strings

Authors Nicola Rizzo , Veli Mäkinen , Nadia Pisanti

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Subject Classification

ACM Subject Classification
  • Theory of computation → Pattern matching
  • Theory of computation → Sorting and searching
  • Theory of computation → Dynamic programming
  • Applied computing → Genomics
Keywords
  • multiple sequence alignment
  • pattern matching
  • data structures
  • segmentation algorithms
  • founder reconstruction
  • dynamic programming
  • semi-dynamic range minimum queries
  • positional Burrows-Wheeler transform

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Abstract

An elastic degenerate string (EDS) is a sequence of sets of strings. In the context of bioinformatics, EDSes can be used to represent the variations observed in a population from its consensus genome. Pattern matching and comparison problems on EDSes have been widely studied in the literature, but their construction has been largely omitted. We fill this gap by showing how algorithms originally developed for related problems of founder reconstruction can be adapted to minimize the total cardinality of the EDS sets and total length of the EDS strings in linear time, given suitable multiple alignments representing the input data.

Cite As Get BibTex

Nicola Rizzo, Veli Mäkinen, and Nadia Pisanti. On the Construction of Elastic Degenerate Strings. In From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 132, pp. 2:1-2:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025) https://doi.org/10.4230/OASIcs.Grossi.2

Author Details

Nicola Rizzo
  • Department of Computer Science, University of Helsinki, Finland
Veli Mäkinen
  • Department of Computer Science, University of Helsinki, Finland
Nadia Pisanti
  • Universitá di Pisa, Italy

Funding

This work was partially supported by the PANGAIA, ALPACA, and TeamPerMed projects that received funding from the European Union’s Horizon 2020 research and innovation programme with two first under the Marie Skłodowska-Curie grant agreements No. 872539 and 956229, respectively, and the third under grant agreement No. 101060011. NP was also partially supported by MUR PRIN 2022 YRB97K PINC.

References

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