Search Results for author: Gonzalo Navarro

Found 7 papers, 5 papers with code

A grammar compressor for collections of reads with applications to the construction of the BWT

1 code implementation13 Nov 2020 Diego Díaz-Domínguez, Gonzalo Navarro

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

Grammar-Compressed Indexes with Logarithmic Search Time

1 code implementation1 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

Cell cycle and protein complex dynamics in discovering signaling pathways

no code implementations26 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.

Fast, Small, and Simple Document Listing on Repetitive Text Collections

no code implementations20 Feb 2019 Dustin Cobas, Gonzalo Navarro

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


Faster Repetition-Aware Compressed Suffix Trees based on Block Trees

1 code implementation8 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

On the Approximation Ratio of Greedy Parsings

2 code implementations26 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

Compressed Text Indexes:From Theory to Practice!

6 code implementations20 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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