20 citations · 52 across the 18 of their papers we have counts for
4 papers · 1 filter
Finding Maximal Exact Matches in Graphs
Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
We study the problem of finding maximal exact matches (MEMs) between a query string and a labeled graph . MEMs are an important class of seeds, often used in seed-chain-exte…
Elastic Founder Graphs Improved and Enhanced
Nicola Rizzo, Massimo Equi, Tuukka Norri +1
Indexing labeled graphs for pattern matching is a central challenge of pangenomics. Equi et al. (Algorithmica, 2022) developed the Elastic Founder Graph () representi…
From Bit-Parallelism to Quantum String Matching for Labelled Graphs
Massimo Equi, Arianne Meijer - van de Griend, Veli Mäkinen
Many problems that can be solved in quadratic time have bit-parallel speed-ups with factor , where is the computer word size. A classic example is computing the edit distanc…
Chaining of Maximal Exact Matches in Graphs
Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
We show how to chain maximal exact matches (MEMs) between a query string and a labeled directed acyclic graph (DAG) to solve the longest common subsequence (LCS) prob…