Results 31 to 40 of about 679,088 (213)

More Time-Space Tradeoffs for Finding a Shortest Unique Substring

Algorithms, 2020
We extend recent results regarding finding shortest unique substrings (SUSs) to obtain new time-space tradeoffs for this problem and the generalization of finding k-mismatch SUSs.
Hideo Bannai, Travis Gagie, Gary Hoppenworth, Simon J. Puglisi, Luís M. S. Russo   +4 more
doaj   +1 more source

Suffix Tree

, 2009
International ...
Crochemore, Maxime, Lecroq, Thierry
openaire   +3 more sources

Suffix Trees for Document Retrieval [PDF]

, 2012
This thesis presents a look at the suitability of Suffix Trees for full text indexing and retrieval. Typically suffix trees are built on a character level, where the tree records which characters follow each other character.
Reck, Ryan
core   +1 more source

Local Similarity Search to Find Gene Indicators in Mitochondrial Genomes

Biology, 2014
Given a set of nucleotide sequences we consider the problem of identifying conserved substrings occurring in homologous genes in a large number of sequences.
Ruby L. V. Moritz, Matthias Bernt, Martin Middendorf   +2 more
doaj   +1 more source

Analyzing State Sequences with Probabilistic Suffix Trees: The PST R Package

Journal of Statistical Software, 2016
This article presents the PST R package for categorical sequence analysis with probabilistic suffix trees (PSTs), i.e., structures that store variable-length Markov chains (VLMCs).
Alexis Gabadinho, Gilbert Ritschard
doaj   +1 more source

The afterlife of a horizontally transferred gene: Expansion and functional diversification of a C1A peptidase in wild Hordeum species. [PDF]

Plant Genome
Abstract Horizontal gene transfer (HGT) can accelerate plant adaptation, but the evolutionary fate of newly acquired nuclear genes is often unclear. Here, we analyzed a papain‐like cysteine peptidase horizontally transferred from Panicoideae to wild Hordeum (Poaceae). Using chromosome‐level assemblies of 21 diploid Hordeum species, we assessed presence/
Mahelka V, Caklová P, Čegan R, Villanueva-Corrales S, Josefiová J, Kneřová J, Kopecký D, Nagy-Nejedlá M, Szecówka M, Krak K.   +9 more
europepmc   +2 more sources

An Algorithm for Identifying Novel Targets of Transcription Factor Families: Application to Hypoxia-inducible Factor 1 Targets

Cancer Informatics, 2009
Efficient and effective analysis of the growing genomic databases requires the development of adequate computational tools. We introduce a fast method based on the suffix tree data structure for predicting novel targets of hypoxia-inducible factor 1 (HIF-
Yue Jiang, Bojan Cukic, Donald A. Adjeroh, Heath D. Skinner, Jie Lin, Qingxi J. Shen, Bing-Hua Jiang   +6 more
doaj   +2 more sources

Construction of distributed suffix trees

Технічна інженерія
The paper addresses the problem of parallel suffix tree construction over large text arrays without the use of cluster infrastructure. The evolution of relevant algorithms is analysed – from the single-threaded methods of Weiner, McCreight, and Ukkonen ...
D.V. Zvazhii, O.M. Malii
doaj   +1 more source

Representing the suffix tree with the CDAWG

CoRR, 2017
Given a string $T$, it is known that its suffix tree can be represented using the compact directed acyclic word graph (CDAWG) with $e_T$ arcs, taking overall $O(e_T+e_{\overline{T}})$ words of space, where ${\overline{T}}$ is the reverse of $T$, and supporting some key operations in time between $O(1)$ and $O(\log{\log{n}})$ in the worst case.
Belazzougui, Djamal, Cunial, Fabio
openaire   +5 more sources

Suffix trees for very large inputs [PDF]

, 2010
A suffix tree is a fundamental data structure for string searching algorithms. Unfortunately, when it comes to the use of suffix trees in real-life applications, the current methods for constructing suffix trees do not scale for large inputs.
Barsky, Marina
core   +1 more source