Results 1 to 10 of about 5,370 (228)
ntStat: k-mer characterization using occurrence statistics in raw sequencing data. [PDF]
PLoS Computational BiologyK-mer counts are fundamental in many genomic data analysis tasks, providing valuable information for genome assembly, error correction, and variant detection.
Parham Kazemi +3 more
doaj +2 more sources
A comparison study of succinct data structures for use in GWAS. [PDF]
BMC Bioinformatics, 2013 In recent years genetic data analysis has seen a rapid increase in the scale of data to be analyzed. Schadt et al (NRG 11:647-657, 2010) offered that with data sets approaching the petabyte scale, data related challenges such as formatting, management, and transfer are increasingly important topics which need to be addressed.
Putnam PP, Zhang G, Wilsey PA.
europepmc +4 more sources
Application-Oriented Succinct Data Structures for Big Data [PDF]
The Review of Socionetwork Strategies, 2019 Abstract A data structure is called succinct if its asymptotical space requirement matches the original data size. The development of succinct data structures is an important factor to deal with the explosively increasing big data.
Tetsuo Shibuya, Shibuya Tetsuo
exaly +2 more sources
Rank and Select for Succinct Data Structures
Electronic Notes in Theoretical Computer Science, 2009 AbstractIn this paper, we study different approaches for rank and select on sequences of bytes and propose new implementation strategies. Extensive experimental evaluation comparing the efficiency of the different alternatives are provided.Given a sequence of bits, a rank query counts the number of occurrences of the bit 1 up to a given position, and a
OSCAR Pedreira +2 more
exaly +2 more sources
BSuccinct: Rust libraries and programs focused on succinct data structures
SoftwareXBSuccinct is a collection of software focused on compact and succinct data structures that are both space and time efficient. It is written in Rust, a programming language well suited for scientific applications due to its emphasis on reliability and ...
Piotr Beling
doaj +3 more sources
Succinct data structures for nearest colored node in a tree
Information Processing Letters, 2018 We give a succinct data-structure that stores a tree with colors on the nodes. Given a node x and a color alpha, the structure finds the nearest node to x with color alpha. This results improves the $O(n\log n)$-bits structure of Gawrychowski et al.~[CPM 2016].
Dekel Tsur
exaly +4 more sources
Buffering updates enables efficient dynamic de Bruijn graphs
Computational and Structural Biotechnology Journal, 2021 Motivation: The de Bruijn graph has become a ubiquitous graph model for biological data ever since its initial introduction in the late 1990s. It has been used for a variety of purposes including genome assembly (Zerbino and Birney, 2008; Bankevich et al.
Jarno Alanko +4 more
doaj +1 more source
Computing RF Tree Distance over Succinct Representations
Algorithms, 2023 There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks or cancerous cells in tumor progression trees.
António Pedro Branco +2 more
doaj +1 more source
Succinct data structure for path graphs
Information and Computation, 2022 We consider the problem of designing a succinct data structure for {\it path graphs} (which are a proper subclass of chordal graphs and a proper superclass of interval graphs) on $n$ vertices while supporting degree, adjacency, and neighborhood queries efficiently. We provide the following two solutions for this problem: - an $n \log n+o(n \log n)$-bit
Girish Balakrishnan +3 more
openaire +3 more sources
Dynamic community discovery via common subspace projection
New Journal of Physics, 2021 Detecting communities of highly internal and low external interactions in dynamically evolving networks has become increasingly important owing to its wide applications in divers fields.
Lanlan Yu +3 more
doaj +1 more source