5 citations · 7 across the 6 of their papers we have counts for
10 papers · 1 filter
Adaptive encodings for small and fast compressed suffix arrays
Diego Díaz-Domínguez, Veli Mäkinen
Compressed suffix arrays (CSAs) index large repetitive collections and are key in many text applications. The r-index and its derivatives combine the run-length Burrows-Wheeler Tra…
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…
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…
Tailoring r-index for metagenomics
Dustin Cobas, Veli Mäkinen, Massimiliano Rossi
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metageno…
Linear Time Construction of Indexable Founder Block Graphs
Veli Mäkinen, Bastien Cazaux, Massimo Equi +2
We introduce a compact pangenome representation based on an optimal segmentation concept that aims to reconstruct founder sequences from a multiple sequence alignment (MSA). Such f…