> Detailanzeige

Equi, Massimo [VerfasserIn]; Norri, Tuukka [VerfasserIn]; Alanko, Jarno [VerfasserIn]; Cazaux, Bastien [VerfasserIn]; Tomescu, Alexandru I. [VerfasserIn]; Mäkinen, Veli [VerfasserIn] ; Massimo Equi and Tuukka Norri and Jarno Alanko and Bastien Cazaux and Alexandru I. Tomescu and Veli Mäkinen [MitwirkendeR]

Algorithms and Complexity on Indexing Elastic Founder Graphs

Literatur-
verwaltung

Zur
Merkliste

Lösche von
Merkliste

Per Whatsapp teilen

Schließen

Merkliste



Sie können Bookmarks mittels Listen verwalten, loggen Sie sich dafür bitte in Ihr SLUB Benutzerkonto ein.
  • Medientyp: E-Artikel; Sonstige Veröffentlichung; Elektronischer Konferenzbericht
  • Titel: Algorithms and Complexity on Indexing Elastic Founder Graphs
  • Beteiligte: Equi, Massimo [VerfasserIn]; Norri, Tuukka [VerfasserIn]; Alanko, Jarno [VerfasserIn]; Cazaux, Bastien [VerfasserIn]; Tomescu, Alexandru I. [VerfasserIn]; Mäkinen, Veli [VerfasserIn]
  • Erschienen: Schloss Dagstuhl – Leibniz-Zentrum für Informatik, 2021
  • Sprache: Englisch
  • DOI: https://doi.org/10.4230/LIPIcs.ISAAC.2021.20
  • Schlagwörter: segmentation ; multiple sequence alignment ; orthogonal vectors hypothesis
  • Entstehung:
  • Anmerkungen: Diese Datenquelle enthält auch Bestandsnachweise, die nicht zu einem Volltext führen.
  • Beschreibung: We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in polynomial time to answer queries efficiently (Equi et al. ICALP 2019, SOFSEM 2021). These conditional lower-bounds cover even deterministic graphs with binary alphabet, but there naturally exist also graph classes that are easy to index: E.g. Wheeler graphs (Gagie et al. Theor. Comp. Sci. 2017) cover graphs admitting a Burrows-Wheeler transform -based indexing scheme. However, it is NP-complete to recognize if a graph is a Wheeler graph (Gibney, Thankachan, ESA 2019). We propose an approach to alleviate the construction bottleneck of Wheeler graphs. Rather than starting from an arbitrary graph, we study graphs induced from multiple sequence alignments. Elastic degenerate strings (Bernadini et al. SPIRE 2017, ICALP 2019) can be seen as such graphs, and we introduce here their generalization: elastic founder graphs. We first prove that even such induced graphs are hard to index under OVH. Then we introduce two subclasses that are easy to index. Moreover, we give a near-linear time algorithm to construct indexable elastic founder graphs. This algorithm is based on an earlier segmentation algorithm for gapless multiple sequence alignments inducing non-elastic founder graphs (Mäkinen et al., WABI 2020), but uses more involved techniques to cope with repetitive string collections synchronized with gaps. Finally, we show that one of the subclasses admits a reduction to Wheeler graphs in polynomial time.
  • Zugangsstatus: Freier Zugang