5 citations · 8 across the 10 of their papers we have counts for
4 papers · 1 filter
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…
Graphs cannot be indexed in polynomial time for sub-quadratic time string matching, unless SETH fails
Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu
We consider the following string matching problem on a node-labeled graph : given a pattern string , decide whether there exists a path in whose concatenation of no…
Chaining with overlaps revisited
Veli Mäkinen, Kristoffer Sahlin
Chaining algorithms aim to form a semi-global alignment of two sequences based on a set of anchoring local alignments as input. Depending on the optimization criteria and the exact…