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 …

Algorithmics on SLP-compressed strings: A survey

M Lohrey - Groups-Complexity-Cryptology, 2012 - degruyter.com
Results on algorithmic problems on strings that are given in a compressed form via straight-
line programs are surveyed. A straight-line program is a context-free grammar that …

Searching and indexing genomic databases via kernelization

T Gagie, SJ Puglisi - Frontiers in Bioengineering and Biotechnology, 2015 - frontiersin.org
The rapid advance of DNA sequencing technologies has yielded databases of thousands of
genomes. To search and index these databases effectively, it is important that we take …

A faster grammar-based self-index

T Gagie, P Gawrychowski, J Kärkkäinen… - … on Language and …, 2012 - Springer
To store and search genomic databases efficiently, researchers have recently started
building compressed self-indexes based on straight-line programs and LZ77. In this paper …

LZ77-based self-indexing with faster pattern matching

T Gagie, P Gawrychowski, J Kärkkäinen… - Latin American …, 2014 - Springer
To store and search genomic databases efficiently, researchers have recently started
building self-indexes based on LZ77. As the name suggests, a self-index for a string …

Faster fully compressed pattern matching by recompression

A Jeż - ACM Transactions on Algorithms (TALG), 2015 - dl.acm.org
In this article, a fully compressed pattern matching problem is studied. The compression is
represented by straight-line programs (SLPs)—that is, context-free grammars generating …

Improved grammar-based compressed indexes

F Claude, G Navarro - International Symposium on String Processing and …, 2012 - Springer
We introduce the first grammar-compressed representation of a sequence that supports
searches in time that depends only logarithmically on the size of the grammar. Given a text T …

Semi-local string comparison: Algorithmic techniques and applications

A Tiskin - Mathematics in Computer Science, 2008 - Springer
Given two strings, the longest common subsequence (LCS) problem consists in computing
the length of the longest string that is a subsequence of both input strings. Its generalisation …

Colored range queries and document retrieval

T Gagie, J Kärkkäinen, G Navarro, SJ Puglisi - Theoretical Computer …, 2013 - Elsevier
Colored range queries are a well-studied topic in computational geometry and database
research that, in the past decade, have found exciting applications in information retrieval. In …

[HTML][HTML] Fast relative Lempel–Ziv self-index for similar sequences

HH Do, J Jansson, K Sadakane, WK Sung - Theoretical Computer Science, 2014 - Elsevier
Recent advances in biotechnology and web technology are continuously generating huge
collections of similar strings. People now face the problem of storing them compactly while …