Results 101 to 110 of about 4,379 (204)
Massively parallel suffix array construction [PDF]
, 1998 This paper considers the construction of the suffix array of a string on the MasPar MP-2 architecture. Suffix arrays are space-efficient variants of the suffix trees, a fundamental dictionary data structure that is the backbone of many string algorithms ...
Rovan, B, Korda, M
core
The enhanced suffix array yields a tree structure of nested suffix intervals. [PDF]
, 2013 The enhanced suffix array for the sequence S: = attcttcggc (left) and its suffix interval tree (right), equivalent to the suffix trie in Fig. 2, is shown. The array suf represents the lexicographical order of the suffixes in S$.
Cynthia M. Sharma (95322) +7 more
core +1 more source
Speeding up tandem mass spectrometry-based database searching by longest common prefix
BMC Bioinformatics, 2010 Background Tandem mass spectrometry-based database searching has become an important technology for peptide and protein identification. One of the key challenges in database searching is the remarkable increase in computational demand, brought about by ...
Wang Le-Heng +7 more
doaj +1 more source
Suffix Tree Construction and Storage with Limited Main Memory [PDF]
, 2003 Schürmann K-B, Stoye J. Suffix Tree Construction and Storage with Limited Main Memory. Forschungsberichte. Bielefeld: Technische Fakultät der Universität Bielefeld; 2003.Suffix trees have been established as one of the most versatile index structures for
Schürmann, Klaus-Bernd +1 more
core +1 more source
Compact and hash based variants of the suffix array [PDF]
, 2017 Full-text indexing aims at building a data structure over a given text capable of efficiently finding arbitrary text patterns, and possibly requiring little space. We propose two suffix array inspired full-text indexes.
Raniszewski, M. +3 more
core +1 more source
Kohdista: an efficient method to index and query possible Rmap alignments
Algorithms for Molecular Biology, 2019 Background Genome-wide optical maps are ordered high-resolution restriction maps that give the position of occurrence of restriction cut sites corresponding to one or more restriction enzymes. These genome-wide optical maps are assembled using an overlap-
Martin D. Muggli +2 more
doaj +1 more source
A taxonomy of suffix array construction algorithms [PDF]
, 2005 In 1990 Manber & Myers proposed suffix arrays as a space-saving alternative to suffix trees and described the first algorithms for suffix array construction and use.
Smyth, W.F., Turpin, A., Puglisi, S.J.
core
In-place update of suffix array while recoding words [PDF]
, 2008 International audienceMotivated by grammatical inference and data compression applications, we propose an algorithm to update a suffix array while in the indexed text some occurrences of a given word are substituted by a new character.
Coste, François +2 more
core +2 more sources
StreamAligner: a streaming based sequence aligner on Apache Spark
Journal of Big Data, 2018 Next-Generation Sequencing technologies are generating a huge amount of genetic data that need to be mapped and analyzed. Single machine sequence alignment tools are becoming incapable or inefficient in keeping track of the same.
Sanjay Rathee, Arti Kashyap
doaj +1 more source
XenDB: Full length cDNA prediction and cross species mapping in
BMC Genomics, 2005 Background Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers.
Giegerich Robert +4 more
doaj +1 more source