Results 11 to 20 of about 301,848 (186)
Replacing suffix trees with enhanced suffix arrays [PDF]
Journal of Discrete Algorithms, 2004 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Stefan Kurtz, Enno Ohlebusch
exaly +3 more sources
Counting Suffix Arrays and Strings [PDF]
Theoretical Computer Science, 2005 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Schürmann, Klaus-Bernd, Stoye, Jens
core +6 more sources
Efficient computation of absent words in genomic sequences [PDF]
BMC Bioinformatics, 2008 Background Analysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so on.
Herold Julia +2 more
doaj +2 more sources
Dynamic extended suffix arrays [PDF]
Journal of Discrete Algorithms, 2010 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Salson, Mikael +3 more
openaire +7 more sources
RECONSTRUCTING A SUFFIX ARRAY [PDF]
International Journal of Foundations of Computer Science, 2006 For certain problems (for example, computing repetitions and repeats, data compression applications) it is not necessary that the suffixes of a string represented in a suffix tree or suffix array should occur in lexicographical order (lexorder). It thus becomes of interest to study possible alternate orderings of the suffixes in these data structures,
Franěk, F., Smyth, W.F.
openaire +3 more sources
Fast Hybrid Data Structure for a Large Alphabet K-Mers Indexing for Whole Genome Alignment
IEEE Access, 2021 The most common index data structures used by whole genome aligners (WGA) are based on suffix trees (ST), suffix arrays, and FM-indexes. These data structures show good performance results as WGA works with sequences of letters over small alphabets; for ...
Rostislav Hrivnak +2 more
doaj +1 more source
Suffix arrays in theory and practice. [PDF]
, 2007 The suffix array of a string is a permutation of all starting positions of the string's suffixes in lexicographical order. In this thesis, we investigate mathematical and algorithmical aspects of suffix arrays. The first part mainly deals with combinatorial properties of suffix arrays and their enumeration.
Schürmann, Klaus-Bernd
openaire +3 more sources
GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array. [PDF]
PLoS ONE, 2014 DNA sequences are translated into protein coding sequences and then further assigned to protein families in metagenomic analyses, because of the need for sensitivity.
Shuji Suzuki +3 more
doaj +1 more source
Computing and Informatics, 2019 The suffix array is a classic full-text index, combining effectiveness with simplicity. We discuss three approaches aiming to improve its efficiency even more: changes to the navigation, data layout and adding extra data. In short, we show that i) the way how we search for the right interval boundary impacts significantly the overall search speed, ii ...
Kowalski, Tomasz M. +2 more
openaire +2 more sources
Suffix Arrays in Parallel [PDF]
, 2003 Suffix arrays are powerful data structures for text indexing. In this paper we present parallel algorithms devised to increase throughput of suffix arrays on a multiple-query setting. Experimental results show that efficient performance is indeed feasible in this strongly sequential and very poor locality data structure.
Mauricio Marín, Gonzalo Navarro 0001
openaire +2 more sources