Fully functional suffix trees and optimal text searching in BWT-runs bounded space
Indexing highly repetitive texts—such as genomic databases, software repositories and
versioned text collections—has become an important problem since the turn of the …
versioned text collections—has become an important problem since the turn of the …
Space-efficient preprocessing schemes for range minimum queries on static arrays
J Fischer, V Heun - SIAM Journal on Computing, 2011 - SIAM
Given a static array of n totally ordered objects, the range minimum query problem is to build
a data structure that allows us to answer efficiently subsequent on-line queries of the form …
a data structure that allows us to answer efficiently subsequent on-line queries of the form …
Optimal-time text indexing in BWT-runs bounded space
Indexing highly repetitive texts—such as genomic databases, software repositories and
versioned text collections—has become an important problem since the turn of the …
versioned text collections—has become an important problem since the turn of the …
On compressing and indexing repetitive sequences
S Kreft, G Navarro - Theoretical Computer Science, 2013 - Elsevier
We introduce LZ-End, a new member of the Lempel–Ziv family of text compressors, which
achieves compression ratios close to those of LZ77 but is much faster at extracting arbitrary …
achieves compression ratios close to those of LZ77 but is much faster at extracting arbitrary …
Pan-genome storage and analysis techniques
Computational pan-genome analysis has emerged from the rapid increase of available
genome sequencing data. Starting from a microbial pan-genome, the concept has spread to …
genome sequencing data. Starting from a microbial pan-genome, the concept has spread to …
Indexing variation graphs
J Sirén - 2017 Proceedings of the ninteenth workshop on …, 2017 - SIAM
Variation graphs, which represent genetic variation within a population, are replacing
sequences as reference genomes. Path indexes are one of the most important tools for …
sequences as reference genomes. Path indexes are one of the most important tools for …
Alphabet-independent compressed text indexing
D Belazzougui, G Navarro - ACM Transactions on Algorithms (TALG), 2014 - dl.acm.org
Self-indexes are able to represent a text asymptotically within the information-theoretic lower
bound under the k th order entropy model and offer access to any text substring and indexed …
bound under the k th order entropy model and offer access to any text substring and indexed …
Prospects and limitations of full-text index structures in genome analysis
M Vyverman, B De Baets, V Fack… - Nucleic acids …, 2012 - academic.oup.com
The combination of incessant advances in sequencing technology producing large amounts
of data and innovative bioinformatics approaches, designed to cope with this data flood, has …
of data and innovative bioinformatics approaches, designed to cope with this data flood, has …
Optimal succinctness for range minimum queries
J Fischer - Latin American Symposium on Theoretical Informatics, 2010 - Springer
For a static array A of n totally ordered objects, a range minimum query asks for the position
of the minimum between two specified array indices. We show how to preprocess A into a …
of the minimum between two specified array indices. We show how to preprocess A into a …
Fully compressed suffix trees
Suffix trees are by far the most important data structure in stringology, with a myriad of
applications in fields like bioinformatics and information retrieval. Classical representations …
applications in fields like bioinformatics and information retrieval. Classical representations …