1 code implementation • 13 Nov 2020 • Diego Díaz-Domínguez, Gonzalo Navarro

We describe a grammar for DNA sequencing reads from which we can compute the BWT directly.

1 code implementation • 1 Apr 2020 • Francisco Claude, Gonzalo Navarro, Alejandro Pacheco

Let a text $T[1.. n]$ be the only string generated by a context-free grammar with $g$ (terminal and nonterminal) symbols, and of size $G$ (measured as the sum of the lengths of the right-hand sides of the rules).

Data Structures and Algorithms

no code implementations • 26 Feb 2020 • Daniel Inostroza, Cecilia Hernández, Diego Seco, Gonzalo Navarro, Alvaro Olivera-Nappa

Signaling pathways are responsible for the regulation of cell processes, such as monitoring the external environment, transmitting information across membranes, and making cell fate decisions.

no code implementations • 20 Feb 2019 • Dustin Cobas, Gonzalo Navarro

Document listing on string collections is the task of finding all documents where a pattern appears.

1 code implementation • 8 Feb 2019 • Manuel Cáceres, Gonzalo Navarro

Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications.

Data Structures and Algorithms E.1; E.4; H.3

2 code implementations • 26 Mar 2018 • Gonzalo Navarro, Nicola Prezza

We prove that the size v of the smallest parse of this kind has properties similar to z, including the same approximation ratio with respect to b. Interestingly, we also show that v = O(r), whereas r = o(z) holds on some particular classes of strings.

Data Structures and Algorithms

6 code implementations • 20 Dec 2007 • Paolo Ferragina, Rodrigo Gonzalez, Gonzalo Navarro, Rossano Venturini

A compressed full-text self-index represents a text in a compressed form and still answers queries efficiently.

Data Structures and Algorithms F.2.2; H.2.1; H.3.2; H.3.3

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