4 papers
Quantum Pattern Matching in Generalised Degenerate Strings
Massimo Equi, Md Rabiul Islam Khan, Veli Mäkinen
A degenerate string is a sequence of sets of characters. A generalized degenerate (GD) string extends this notion to the sequence of sets of strings, where strings of the same set…
Adaptive encodings for small and fast compressed suffix arrays
Diego DÃaz-DomÃnguez, 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…
Practical colinear chaining on sequences revisited
Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Colinear chaining is a classical heuristic for sequence alignment and is widely used in modern practical aligners. Jain et al. (J. Comput. Biol. 2022) proposed an t…
On the compressiveness of the Burrows-Wheeler transform
Hideo Bannai, Tomohiro I, Yuto Nakashima
The Burrows-Wheeler transform (BWT) is a reversible transform that converts a string into another string . The size of the run-length encoded BWT (RLBWT) can b…